I have read about people having trouble with Timbermate and water based stain, as well as shrinkage with some paints, but I have to say I've not encountered these issues.
This ash Tele (TLA-1 kit) is ebony Timbermate and water based dye (ColorTone and U-Beaut) with DIY wipe-on poly.
Attachment 35342
And this Stra-Tele is Timbermate under acrylic lacquer (over basswood).
Attachment 35344
Neither one gave me any problems (apart from the Stra-Tele which got painted 3 times due to other paint difficulties :mad:)