I'm using Roll20 to play a skirmish boardgame I'm designing and currently playtesting. The game uses a modular board that may be similar to what you're interested in. If you search for the keyword Streets-of-Ruin for tokens the tiles for the game should come up. I give GM permissions to my playtesters. The first stage of the game is constructing the modular board, which consists of 9 7" x 7" gridded tiles. It takes us about 5 - 10 minutes to choose tiles, rotate, and place them to construct the board...and constructing the board is a critical part of the game due to the important of terrain types.
Just my two sense. Roll20 seems ok at this already, though I'd love an implementations of a modular board design system.