Yes, all changeovers on GWR are manual. APCO has been considered but there are so many parameters/complications that it wouldn't be possible to have all changeovers carried out automatically, and having a mix of manual and automatic changeovers is a recipe for operational incidents.
There are Eurobalises (ETCS balises) in places, yes, but these are what's known as 'zero balises' which tell the train to lower the pan automatically if the driver forgets to do so. There will also be balises appearing for BBASDO (Balise-Based ASDO which uses Eurobalises to determine platform number, and therefore enables correct side door enable (CSDE), which inhibits wrong-side door releases), and of course there are balises being installed on the route out of Paddington for ETCS Level 2.
Strictly speaking, the engines on 80x should only be started if the coolant temp. is 45 degrees or more. The coolant can be pre-heated via the TMS, but GWR have told Hitachi that using the TMS to start the pre-heat and then monitoring the temperatures, all while running at up to 125mph is too much of a distraction risk, so drivers are instructed to just press the diesel button at the changeover location (although some drivers just begin the pre-heat at the start of the journey while on electric). If the engines are cold, then they will idle until the coolant warms up. If APCO were operational, the engine pre-heat would begin at a distance from the changeover location (4 miles IIRC) - the headcode data that includes the stopping pattern, times etc. can also - if included in the database - include changeover locations and GPS co-ordinates for the engine pre-heat to begin.
Dynamic power changeover for GWR 769s is carried out at Shalford Jct when switching from diesel to DC when coming from Redhill/Gatwick, but statically at Guildford for trains heading towards Redhill/Gatwick. This is because the changeover from diesel to DC is much quicker and therefore has less of a distraction risk than changing from DC to diesel, and because changing from DC to diesel dynamically prior to Shalford Jct would basically mean doing so in a tunnel. So eastbound trains (heading to Redhill/Gatwick) will run on diesel in the tunnels, but trains in the opposite direction (towards Reading) won't.
Dynamic changeovers are also approved at Ash (DC to diesel) and Aldershot Sth Jct (diesel to DC) for trains not booked to call at Ash, and at Reading Spur Jct (DC to diesel and vice versa) for trains heading to/from the higher number platforms at Reading via the Low Level line.