Shrug.
1) Protos are fluffed as being resource efficient.
2) The Scorps had plenty of time to get the relevant machinery and tooling off Roche, and if they were unsure of their resource situation in Castillian Space, it would make sense to prioritise bringing that machinery.
3) They made it a point to bring a large supply of excess Protomech AC8s with them, which is why the Reptar initially was armed with it.
4) The Crimson Seeker book highlighted that one of the top Seeker units going into the Dark Age had an elite Protomech pilot with Society tech.
5) The large facility on Navarre (I believe) was fluffed as absolutely huge, and if you already brought the tooling it would be efficient to add a Proto line and take advantage of the huge training and logistics operation being set up.
So, lets be honest, a case can be made either way that Protos do or do not make sense for the Empire. It is 100% a question of Developer and Authour taste. I am of the opinion that the vision set out by Eliot Want in Spotlight on Crimson Seekers should have been expanded on, because big changes in the unit directions that are hinted in one publication, and then substantially changed in another constitute a big change in the flavor of a faction that give fans unneeded whiplash.