It is almost certainly true that the AT300 series units will accelerate faster, at least under the wires, than IC125s. But this was, apparently, not considered too great a problem from August 2011 (when I'm sure Modern Railways stated that IC125s would remain on the PAD-Plymouth/Penzance services, with IEP on the Oxford/Bristol/Swansea routes) to shortly before the new franchise agreement which brought the branding change to GWR. Even when that deal was introduced, there were two Service Level Commitment options for post-2018, the first of which assumed continued operation of IC125s on the PAD-PLY/PNZ route. I seem to recall reading on one forum or other that it had been decided the power-door mrk3s were unaffordable and hence the order for class 802s.
This is exactly my point, rather than reducing train lengths to 5-car class 802 on many PAD-PLY/PNZ services, I feel the 2+8 IC125s should be retained on the PAD-PLY/PNZ route. That August 2011 Modern Railways also stated that stakeholders did not want the underfloor-engined class 222 units for such a long route, so it makes more sense to me to use the 5-car 800s and/or 802s on regional express services where fewer passengers will be going long distances and where 5 coaches is an increase in capacity, rather than a reduction as it would be on GW INTERCITY routes.
What I've read online (or perhaps in Modern Railways) is that ALL mark 3s are not built to exact dimensions and every one is slightly different (this was discovered while fitting the Chiltern ones with power-doors). That meant Chiltern-style mods were very time consuming and expensive, so FirstGWR decided they would have to order the 802s. However, then it turned out ScotRail had thought of a cheaper way of fitting the plug-doors, so presumably all future mrk3 plug-door convertions, whether of IC125 trailers or LHCS, will use the new technique and not be like Chiltern's. I could be wrong of course because I don't work in the rail industry.
GW IEP is 18x 9-car sets and 32x 5-car sets diagrammed each day if I recall correctly. That's 322 diagrammed vehicles. That's diagrams, to resource that Agility Trains West will I think have a fleet of 21x 9-car and 36x 5-car, or 369 vehicles. That doesn't include the Plymouth/Penzance class 802 order, and on that basis I think it is an overall increase in capacity, HOWEVER, much of the increase seems to be thanks to the planned doubling of frequency between London and Bristol Temple Meads to 4tph, other routes (at least based on the DfT's draft diagrams, which are apparently inoperable in some cases) such as London-Swansea would see less capacity than today. According to Wikipedia, the class 802 fleet for GW is 173 vehicles, a total of 542 new vehicles across the Great Western fleet, but keep in mind that the class 802s are NOT IEP units.
There is some 110mph running on the Bristol-Taunton route I believe.
IC125s on stoppers, 5-car DMUs on IC routes and totally inappropriate 165s with 2+3 seating, no UEGs and 1/3, 2/3 doors on the franchise's premier regional express service :roll::cry::roll: (the latest Modern Railways states that all 166s will now stay at Reading depot, but doesn't mention what would run Cardiff-Portsmouth, so assume it is still planned to be Turbos). What a mess. Cardiff-Portsmouth needs 5-car end-door units, INTERCITY routes mostly need 7-9 coaches and Networker Turbos should NEVER BE USED ON REGIONAL EXPRESS SERVICES.
Things have changed significantly since the initial rolling stock plans for the post electrification GWML. Just this month, we've just seen the plans for the commuter stock changing yet again, with a net result that even more new stock and even more seats are being provided.
I'm half convinced the RMT only supported a Brexit in the hope it would stop passenger growth so we could all catch our breathes. It's just never ending, and I really don't envy TOC staff who see more passengers going through their stations and on their trains on a daily basis than BR would see during special events, like Papal visits and Cup finals.
The original plans for HST stock worked, they don't work now, with yet more IEP/AT300 stock coming into the franchise, and yet more passenger demand expected to come, which is likely to result in some or all of the 5-car IEP/AT300 fleet being extended in due course, or additional 5-car units being ordered.
The pathing plans have changed too - with more 110mph services operated by more Class 387 units, and the effects of pathing more 125mph IEP units on the core electrified GWML routes, HSTs really start to get in the way with their acceleration, and will be unable to couple up to IEP units to add much needed flexibility on diagramming. There's also an issue of maintaining HST stock alongside IEP/AT300 stock, running two fleets out of the same depots is inefficient and ultimately limits the absolute amount of stock which can be operated from those depots.
The delay in electrification

is another reason the plans have changed - there's no time and no flexibility to send stock off to have power doors fitted, retention toilets added before returning to service. The addition of extra capacity by procuring new stock became, essentially, the only realistic option.
5-car units are an important part in balancing capacity and maintenance - we're going back to portion working, and remember, these are 26m vehicles with 270 standard and 45 first seats, which can be doubled up to provide 540 standard and 90 first seats when needed (slightly more than the 9 car variants). There's not always a need for 2+8 HSTs to run into Cornwall, particularly in the winter, whereas different needs in the summer will allow some Oxford turns to be covered by 5 car units and additional 9 car units deployed to the south west.
The Turbo units will be overhauled and be fitted with different interiors before running the Cardiff to Portsmouth services, gaining 2+2 seating, they'll be very much like the ScotRail Turbostars.
You're getting hung up about numbers of vehicles, not capacity. That's a classic mistake, but one people need to stop making. 26m IEP vehicles are not comparable to 23m Mark 3 vehicles. And they're really rather good inside anyway. Voyagers they most certainly are not.