I'll make a note for the development team about a hole dimension compensation tool. It's a good thought.
Is there a development plan for MatterControl published somewhere?
MatterControl's development is decided two weeks at a time. Current bugs, feature requests, and other problems are documented in the MatterControl GitHub repository and the highest priority items (as decided by the lead developers) are assigned to individual coders who work on it for a two-week period we call a "sprint". Issues can be broken down into smaller tasks so they can be distributed and we meet the goal of having all work done in the two-week period.
As such we do not have a long-term development plan, but a fluid structure which allows us to change focus relatively quickly but stay productive.
Do you know how to automatically scale every part in MatterControl?
Assuming you're asking about some kind of batch function that would automatically scale every item in the QUEUE or LIBRARY, that functionality does not exist. The only method of scaling in MatterControl is Edit mode and is for one model at a time: http://wiki.mattercontrol.com/3D_VIEW/Edit#SCALE