Right. If a player can infiltrate the base and steal certain things without raising any suspicions they should be rewarded with the defending player not knowing they were there, or having to stumble upon the fact that they were there.
It's a risk/reward thing, hopefully. "I could sneak in and maybe take a small number of things with relative safety, or I can make the gamble and try to steal more things with the risk being that if I am spotted I must go to a specific region to extract within the time-limit or lose everything". And the defending player has to deck out his FOB with front-line defences (cameras, soldiers, sensors) to make avoiding an alert more difficult for invaders.
I feel like that scenario is probably the case, due to the fact that in the most recent demo the defending player is alerted and his soldiers are actively searching and not on regular patrol,
which you can see soldiers doing in this older gameplay from the invader perspective. So it seems like it works the way you hope it does.