Typically you need to perceive a Target to affect a Target but container (Room,Structure, Boundary) targets seem to circumvent the need of an arcane connection.
Can an T: Room effect affect an invisible individual that is within the room?
i.e InCo to count the number of big toes in the room.
Say no resistance factor but the Invisibility effect is greater magnitude than the T: Room effect
Yes, T:Room will affect everything that the spell is supposed to. No need to sense the things in the room, just an outside wall or floor or its ceiling. Your InCo spell will definitely count all the toes in the room, invisible or not. Prying Eyes (InIm5 Corebook) would not let you see the invisible person in there because it grants no improvements to your sight other than changing its gaze.
I understand your confusion, but I would argue that you are simply mistaken. Below I have tried my best to capitalize the first letter of the word, when I use words in their specific ArM meanings rather than their common english meanings.
Specifically you seem to have the impression that if I stand outside a room and cast a T:Room spell on the room then I would also need to perceive whoever is inside the room in order for my spell to affect them. This mistake seems to stem from your perceiving the person inside the room as being the Target (in the hermetic sense).
However, my impression is that the Target is the Room (or Structure or Boundary) in every hermetic sense of the word. That is, you need to be able to perceive the Room in order to be able to target it (i.e. the room). Whether or not someone is inside the room or not is immaterial since they are not the Target of your spell. (though you may well consider them to be your (lower case) target. Afterall you dont try to count the number of big toes in a room unless you suspect that there are more than 0 big toes are in there).
This may seem odd if you consider a toe-counting spell but consider for example the spell that causes a Structure to crumble, I dont think anyone would argue that the magus who casts the structure crumbling spell needs an AC to everyone inside the structure in order for them to fall when the building collapses, the fall is merely a (natural) consequence of the collapse. Whether or not the mage cast the spell to get at the people inside or not is immaterial in this sense.
Being able to sense the Target, not the target, is what matters for non AC spells. The Target is what is created/modified/controlled/destroyed/etc by the spell, while the target is affected by the effect on the Target. If you are having trouble telling the difference then I will try to explain. All Creo spells the Target is what you create. You must be able to sense where it is being created and that must be within range. The target is what is affected by the creation of the Target.
So for CrIg spells the Target is the fire (base individual, which is bonfire sized or about 1 pace) while the target is what you are creating the fire to damage. For normal sized fire created this way you normally would have to sense the target since the fire is not overly large. However if you created a CrIg spell with Size +2 (so an inferno 10 paces across) you could cast it to a location you could see and affect targets within the blast radius of the spell.
If you used a massively powerful CrTe spell to create a few thousand ton block of stone at Sight range, that block of stone is the Target. Creating it over a castle, town, or army that is your target does not require you to sense any of them. As long as you can see where you want to create the block you are fine. And when it springs into existence and falls onto the target, it does not matter that you could not sense or even know of the existence of them to squish them flat.
Seems good so far. Do you see any problems with this effect?
Map of reveal
InMe 20
R: Touch, D: Conc,T: Structure
You touch a parchment that has the layout of the area that you are in and on it, the location of all intelligent beings will be marked by a unique symbol.
(Base 3: Locate someone within a container (See InCo), +1 Touch, +1 Conc, +3 Structure)
You would need a map/blueprint of the building you are in - and reminder that you can't use 'Structure' as a stand-in for a large area without a building.