I tend to agree with you. Though I'd probably go with a slightly larger solar that would be a combination bedroom/living room/office, modified at need, along with a small studio for consultations and a small room for any apprentice. The reason I said two levels on a tower per magus is that seemed a good dividing line. That way you could have an area easily marked off by a sanctum marker. 700ish square feet on one level is good enough for a +1 Size lab, which seems desirable to me. And another level can be easily marked off with a sanctum marker (leaving a room outside the marked sanctum for consultations).
My understanding is that the kitchens would be in the main house, along with the great hall, library, council chamber, and rooms suitable for guests. I'd also imagine that meals would likely be taken in the great hall (or delivered to the lab when a magus is working hard).
But I'm mindful that there are servants and storage and other "maintenance" rooms. Servants need places to live and work (though admittedly not much in medieval times). I'm also mindful that towers have thick walls and often very small rooms. A fully open tower level (like for a lab) would be relatively spacious. But as soon as you start subdividing it, you'll lose a lot to walls.
But you're probably right. We could fit three magi in a tower if they were willing to share. We could probably put two magi in a longhouse as well. A 20 ft by 100 ft longhouse would give 1000 square feet for each magus, which, as you say, is more than enough space. I can easily drop out a longhouse or two from the map at need.
Excellent point. I totally missed that. I'll make the palisade surround the compound.
One of the reasons I made the place so big is that we'll have upwards of a hundred people living in this complex, with all of the support needed for that many people. That's a small village. It made sense to me to put in a number of outbuildings such as the mill, the barns, the stable, etc. (We'll want the animals inside the palisade during the winter.) It could all be tightened up, for certain. But I also assumed that we'd have space to work with as we're in a fairly remote location.
As for an Aegis covering the compound, Aegis of the Hearth has a Target of "Boundary," which is defined as "everything within a well-defined natural or man-made boundary." Examples given are is the wall of a city or the edge of a village. It seems like the palisade walls should be a perfect boundary however much ground it covers. If a Boundary spell will cover a city, it should be able to cover a village-sized compound without much trouble.