Could the engi 'dont reclaim when paused' behaviour be made an optional setting so people could opt out of the behaviour? I make use of the pause option similar to Tomma where if I'm e.g. power-stalling I'll want to quickly select engineers on-screen and pause them, so may occasionally pause ones that are reclaiming.
Alternatively could there be a new pause hotkey that pauses every unit except engineers with a reclaim order? I'm not sure if this would be feasible though - i.e. you could have it not affect engineers currently reclaiming, but I don't know if it's possible to analyse the command queue to identify cases where an engineer has a move order followed by a reclaim order, or has a reclaim order on a target outside its build range