I think the two spots where units can enter the big structure are what stick out from a delivery standpoint, at least to me. The rest of the structure makes sense to my brain to a degree - it's embedded down into the mountains, but the entrances look like they're also built on top of the mountains, and yet they're simultaneously connecting at ground level, which produces a disconnect.
I think the way I'd personally solve that would be to make it look like the mountains were carved out to build the structure, effectively dropping the "z position" of the building down in height above sea level so that the entrance still was at ground level and the rest of the building was below that, "underground". This would probably require modifying thhe shapes of the surrounding mountains though to get the desired height effect.
(Or you could add stairs at the entrances and give height to the outer walls lining those sections so that someone at ground level would have to climb up to get to the entrances first?)