About the charter, most of the details will have been discussed beforehand by letters. There was relatively few things that were negociable by the prospective members, because of the peculiar nature of the covenant. See the topic Charter Discussions (OOC)
But if you have questions about it, well, that's what that topic was all about! 
The small tower is basically just to keep watch over the valley -- much too small for a sanctum and not a defensible structure. Just large enough for ladders leading to the top, which is made of wood and just large enough for two grogs to stand watch.
As for other potential places for a sanctum, you have essentially your pick. Small or large (-1 to +2 in Size). Round, square or rectangular. Ground floor, upper floor, basement or cave. From no windows at all to almost completely open to the elements. In the main structure or in its own building. Essentially, the covenant has it all.
Based on the description of what kind of sanctum you want, we will negociate what Virtues and Flaws your lab has. And if the covenant cannot pay the Upkeep for it, then l will add a few more flaws. 
Due to the peculiarity of the aura, any room which is not occupied on a permanent basis tends to change its shape and location. The way between two specific rooms can change from one week to the other. 