Unfortunately, FilletSrf does not handle it very well either…
I posted a bug report last week on this and nobody at McNeel seems to care. Its beginning to look like this is just another half-baked feature that that doesn’t really work.
If you look at the result of FilletSrf in your example the surfaces don’t join correctly. And your example is about as simple an example of crossing a same size fillet as it gets. Anything more complicated and FilletSrf fails to produce any result.