Depends on how you work really...
I come from the DAW world, so my approach to writing is "object-based". For me, a sequence is an object, and each sequence represents a part of the song. And my approach to production is a) write; b) bounce to DAW for recording; c) tweak music to match vocal delivery; d) bounce that to DAW, etc.
Once you combine sequences, unless you can undo it (never tried), you now have one big sequence that might need editing later. Is it possible to edit? Sure. But a pain if you're used to dealing with sequences the way I do.
I always say this... the MPC is slanted toward beat makers that write music once, record to it, and done. Not the way I (and many other producers I know) work. Not that either approach is better than the other - just different ways of working.
But in general, any software feature that allows you to do something (order sequences in song mode), and then requires you to permanently change it (combine into one big sequence) to achieve something else (bounce to audio) is a poorly designed feature. The fact that it used to be there in 1.6 is even more

.
I assume the way the new mixer functionality works is the reason it was removed. But IMO it's a poor implementation then, if you can't order sequences in song mode and then track the whole thing to audio.