I wouldn't worry about the anodizing when it comes to drilling and tapping, its a very thin layer. If it was a hard anodize it might give you a problem but these won't be. Once you break through the anodizing the cast plate is pretty soft and easy to work with. I would not let that get in the way of having a nice black baseplate.
If you have the 3" glass you will need to get a 2". The 3" would not fit on the inside without milling the baseplate.
I have not heard from quite a few people on what options they want. I will send out PM's this weekend to those I have not heard. I can wait a while to order the glass windows since they are in the USA but I want to place the order to Stanwax laser for the ILDA boards pretty soon.
This is going to be an exhausting (yet satisfying) few weeks of hard work. Just as I am about to get started on the project my job wants me to work 60-70 hrs a week. But I would rather be complaining about working too much than too little.