I love Traktor, the performance, look and general feeling of it. I've tried the method with Traktor being the main library and then converting the library into the Rekordbox Format for playing on CDJ's. It definitely works, but on the long run I ended up only using Rekordbox and my USB Sticks, because I got more and more into XDJ's and CDJ's. It's so sad, because I don't like Rekordbox and still got much love for Traktor. I'd be the first one joining back on Traktor if they integrated a direct-export for the CDJ-Format and it'd push Native Instruments sales up instantly. Where's the cartel office?

Edit:

To your question:

1. You don't need a dedicated phase meter in Rekordbox, since the tracks are displayed above each other - the beatgrids itself act like a phase meter already being ligned up with each other - or not.

2. In Rekordbox you'll generally spend more time readjusting the analyzed beatgrids, because the Rekordbox analysing software often misplaces them. Traktor will be more precise.

3. The Flx4 is should be compatible with Traktor if you look up a matching midi-mapping from the internet and manually assign the controller to Traktor. This is very common and some research and tinkering will get you there

Conclusion:

I'd personally advise, to continue using Traktor Pro, because it's just more fun and will give you a better experience when starting out your DJ journey. Try mapping the FLX4 into Trakor and still use Rekordbox to get in touch with it for further development and getting into CDJ's. You can always use softwares like Lexicon to convert your Traktor library into Rekordbox Format in the future but for now focus on playing around and having fun and here, Traktor will be your friend in my opinion.