Would this be part of the relocation trip from Komodo to Raja Ampat or vice versa? If so, then it makes sense. Or are you thinking of doing itineraries Maumere to Maurmere before moving elsewhere vs. just moving along from Maumere to Saumlaki? I haven't done the area, but folks I know think its pretty good, but not awesome. It's definitely macro-centric, which is why I haven't gone there. I know some folks who live for more froggies and Rhinos, but I'm kind of over them.
The latest hype is to kind of skip over Alor in order to travel amongst the Forgotten Islands. I think if I owned a boat I would do as few transition itineraries as possible and as many Raja/Triton Bay and Komodo trips as possible. I would have alternate Raja itineraries, too. Everyone goes to the exact same sites. It can be a beatdown when every boat wants the same sites every single day. There are hundreds of dive sites in the book. I recommend you explore those 150 that are ignored and you will find a bunch that can be part of itineraries that others aren't doing. It does take some adventurous types to do exploratory diving since it can be hit and miss. But if you start with Burt and Maurine's book and just do some that aren't everyday sites, you can get some real winners that are uncrowded.
Just my crazy opinion. I dive to the beat of a different drummer.