Boost now works only in the worlds specified in the "boost_worlds" list in the config.yml.
This means Boost can coexist with other game modes on one server without interfering with block breaking, sign clicking or spawn in other worlds.

[Edit]
Note that I have realized this is incomplete as Boost doesn't currently protect player inventories from non-Boost worlds.
[Edit2]
But Multiverse Inventories works well to take care of that. So it can work multi world without problems.