Why do you say Lockerbie has to be served? I can't imagine many people wanting to travel from south Lancashire to Lockerbie or vice versa. Even without this route it has a fantastic service for a village of under 5,000 population
A number of enthusiasts like to think of trains as "binary" - e.g. "this is InterCity"/ "this is not InterCity" - "this train is "Suburban" / "this train is long distance". Really, though, they are often a bit of everything. The Long Distance High Speed service from London often become just another local train stopping at local stations for local passengers when it gets beyond Dundee/ Perth/ Chester/ Plymouth etc. Some smaller places have a much better quality of service than you might think they deserve because there's no "local" service on the line, so Long Distance High Speed stuff stops there instead (Diss, Berwick upon Tweed etc). That's just how it is, and trying to tidy things up to force services to fit a particular box seems a waste of time (e.g. this fixation with everything meeting a certain definition that it might do in Germany)
I think that the Manchester - Glasgow/ Edinburgh services are the "fast" services from Manchester to Preston (compared to the Wigan trains which handle Farnworth/ Moses Gate etc and the Blackpool trains which handle the stops at Adlington/ Chorley etc)...
...but the TPE services become the "slow" services north of Preston, picking up a large percentage of stops at Oxenholme/ Penrith/ Lockerbie (compared to the generally faster London/ Birmingham - Scotland services). However, those London/ Birmingham - Scotland services are the only trains between Warrington and Wigan, which is why they provide a local service there by stopping at both (since there's nothing else to).
Similarly, TPE are the "fast" trains from Liverpool/ Manchester to Leeds/ York, but then the "slow" trains north of York (hence picking up a large proportion of the Northallerton/ Thirsk/ Chester le Street stops, compared to the generally faster London - Newcastle services)
I suppose the question is, if TPE didn't serve Lockerbie (and Chester le Street etc) then what would? Is there space for a "local" service from Carlisle to Glasgow (in between the slow freight struggling up Beattock and the faster Pendolinos on the line)? Would that be a price worth paying to shave a couple of minutes off the TPE service?
And if the Scottish services stopped at Bolton then would they need to be longer to accommodate short distance passengers on PTE-subsidised tickets crowding onto them (given that passengers in Manchester heading to Bolton may well prefer a swanky 397 over the Sprinters that still provide a number of Bolton services but Glasgow passengers have no real alternative, so if they can't get on board because of Bolton passengers then they are stuck). There are/were similar problems at places like Reading and Milton Keynes where "local" passengers obviously prefer the fancy long distance trains to their slower EMUs on "local" services.
You could insist on Bolton being pick up/set down only, but it's only about fifteen minutes from central Manchester so would a Guard really get round in time to check tickets, given that the trains are over a hundred metres long?
My bigger priority for Bolton would be electrification of the Wigan line, permitting faster/ longer trains with better acceleration - since the current timetable means act around half the Manchester - Bolton services are still diesel operated (why spend all that money on wiring a line and then continue to run so many polluting diesels?).