It's telling that those jira tickets are both in the top five most voted on open server tickets and are from 2010 and before. (I know you know this roger, but) TokuMX completely resolves both of them.
Write concurrecy: yes, TokuMX does not have a database level reader/writer lock.
Index Building: yes, fractal trees can write data much more efficiently, so if index building is a problem, I bet TokuMX solves it.
Practically reducing file size: to be honest, I am not sure because due to our great compression, this has not been a general issue for our users. Our reindex command could reduce file size, but I cannot point to examples.
One of our big goals is to address storage issues MongoDB has.