Quite apart from the issues surrounding lengths of platforms, coaches, and trains, which I'll leave to other people to discuss, the trains acquired in each of the three phases will have to have a lot of flexibility.
Phase 1 will include some straight electrics to replace existing older emus and to replace 156s on newly electrified lines such as Barrhead; and some BEMUs for partly electrified lines such as Borders and Fife. At the time of placing the order the achievable rate of electrification will be uncertain, and so therefore will be the relative numbers of EMUs and BEMUs.
Over time, lines will be converted from partially to fully electrified, so there will probably be a need to convert BEMUs to EMUs, ideally finding some other productive use for the weight capacity saved on the batteries.
Phase 2 will be hydrogen trains for remoter lines and some at least of them will need to have sufficient tank capacity for Inverness to Wick and Thurso. On the other hand some of them will do runs like Glasgow to Stranraer, already electrified to Ayr and eventually to Girvan, so they may well have pantographs and transformers. Inverness to Tain is to be wired eventually, the West Highland will have wires to Craigendoran, and even the Kyle line trains, if equipped, will be able to use the wires to Dingwall.
Phase 3 is to replace diesel on trains from the central belt to Aberdeen and Inverness. If these were to be supplied as straight electrics, they would be unusable until at least one of the routes is fully electrified. But the plan is to put in partial electrification first to achieve the earliest possible decarbonisation. Therefore either the phase 3 trains (or some of them) must be initially supplied as BEMUs, or some BEMUs supplied in phase 1 must be temporarily used as inter-city trains.