I can understand that even a generic Allied person isn't going to be allowed into secure areas without a good reason. Especially since they probably will take anything which isn't nailed down, then break out the Maverick suit to cut the nails and take that too.
But equally it feels like a missed opportunity here. There's all these really interesting bases, and your options for exploring them are:
1) Stick to level-0 areas only, perhaps on a courier mission, and even then a trigger-happy guard might shoot you if you don't notice you're being scanned.
2) Do a power restore mission, getting level-3 clearance and free run of the empty base. Decent.
3) Kill everyone, maybe with some stealth first, clone some clearances, then explore the base.
4) Try to get a look around, mainly on the outside, while in a hot CZ.
Some "support" missions to operational bases would be neat - you get a legit clearance (maybe not 3, maybe just 1 or 2!) and your job is "go into the lab, upload this next experimental protocol, download the last results and bring them back" or "help replace a mining extractor by bringing components from around the base to the technician" (sometimes the new one goes wrong and you then have to put out some fires) or "help defend our base while we take the guns offline for maintenance" which is a bit like a CZ but smaller scope - you and the base guards versus a couple of waves of scavengers.
(and if you want to take the opportunity to steal a couple of things which aren't nailed down while no-one's looking, go ahead!)
It'd make them feel more like places to be and less like artificial targets.