JB4 is really the way to go. It can do everything a stand alone controller can do, only better, becuase it's fully integrated. And all the extra safety features come in REALLY HANDY with single turbos. We've saved more customers motors than we can count with the JB4's passive safety systems.
I will chime in with some personal experience. On both my car the boostbox was giving inconsistent performance and doing some odd electrical things. Replaced the voltage regulator on the alternator and still saw the same issues. Went to an EBC for the time being, really enjoy the on-the-fly adjustability. Since then, I have now been getting intermittent alternator codes, so it was likely the alternator itself causing the issues with BB, but still works good enough for the time being. When MHD does offer on the fly load target changes I'll try going back
I use the boostbox. Have never had any trouble with mine, I hide it in the ecu compartment area.
The one difference with the JB4 is that you can be installing your single kit on Monday and be on the dyno making 750 on tuesday. That is simply not the case with an etune. More like Tuesday of the next year. Pay someone to dyno tune your car and most of that gripe goes away.