So, glad to see my points at least brought up some discussion, because all of this will be useful for anyone who is trying to do time related work like looping to a backing track.
As an update to my original post, I have found that there is indeed about a 100 msec delay from bandhelper that Arlo has noted. The more I assessed waveforms and refined my technique for figuring this out, the more consistent that has been. I end up trimming around 160 msec from each track to get it to line up with the tempo...the additional 30ish msec is due to what gets tacked onto my files when rendered to mp3 in FL studio....so I have to remove 30 from the track I am editing, plus an additional 30 to account for the amount that the new render would tack on. Not clear why this occurs...I have inspected all the rendering settings, but another person in a music forum elsewhere had noted the same with their sequencer program, so I think this is native to mp3 rendering. I also find that once I get the tempo lined up between my track and the Bandhelper tempo (as evidenced by my loops being perfectly on time in Loopy HD, which is slave to Bandhelper's clock), that there is a slightly variable amount of MIDI shift I have to make in my MIDI file. it is ballpark around 40-50 msec, give or take. I trigger a MIDI sound event and check it compared to my tempo clicks and it comes in a tad early. A quick calculation allows me to convert that number of msec into "ticks" of offset in MidiEditor, and I am perfectly in line.
Of course, the negative here is that Arlo has now perfected Bandhelper, so I will need to go back and rework all this if I update! All good, better to have Bandhelper running smoothly. Arlo, I will have to see if I find a global msec time shift useful...I tend to line all of these up manually and sometimes I find some variation, but only by maybe 10-15 msec, so may just be my analysis that is flawed.
As an update to my set up, I switched from Quantiloop to Loopy HD. Thought Quantiloop looked like the best choice....I liked the look of the interface. Loopy looks like a kid's app, with its screen full of swirling circles. But Quantiloop was not playing well at ALL with my iPad Pro running Bandhelper. Loopy HD is incredibly stable, once I learned some tricks. The only early negative was it has to "learn" Midi commands, you cannot input CC numbers and associate commands with them initially. I had to create a training MIDI file with CC's 1-127 on the right MIDI channel for Loopy HD, and run that and get the commands in. Once you have done that, you can easily change what each of those commands does, so that is a one time set up. Obviously geared towards the average user who would have a footpedal to train, but I am using background MIDI files.
Anyway, a couple of other quirks I discovered is that putting your iPad in Airplane mode affects timing between apps, so I have done all of my set up in Airplane mode to promote stability in the system. I also found that Loopy HD really needs a full reset between songs. There is a reset command that erases all loops and clears the tempo. I programmed this into the end of each MIDI file, but was still running into a frustrating time drift as I ran through more than one song. What I speculate is that, even though I might reset LOOPY HD with a MIDI command, Bandhelper might still be sending Tempo at the end of the song, so the Tempo does not get reset, and creates some jitter of sorts when you go to the next song. My solution is a "null" song on my setlist called RESET LOOPY which contains no Tempo, just a MIDI preset with the command to reset Loopy. This works perfectly, and I now have a stable running system.
Loopy is now replacing my Pigtronix Infinity pedal as my looper. First gig is this weekend. I have yet to tap the full potential of this...Loopy can handle 12 loops on top of the overdubs. Pretty incredible. It has take some work and frustration with me ready to pull my hair out a few times, but this is by far the best looping solution out there...way better than any available hardware looper. I am using RME Babyface Pro as my iPad audio interface, and it works great. I use the associated app on my iPad to tweak levels from my two looping sources (guitar, and a separate channel of my guitar as bass after running it through a Whammy and EQ). I also use Audiobus to get my audio into Loopy HD. It has a MIDI function as well, but I was finding some issues using that to help with MIDI between Bandhelper and Loopy HD. I might go back and recheck that now that I understand more, but bottom line is that Bandhelper and LoopyHD talk MIDI just fine, and I see no advantage to Audiobus for the MIDI. One thing that definitely happened was I had it all set up wrong when I was using Audiobus, and my hardware pedals were getting 2 MIDI clock signals, which doubled their tempo. Bandhelper sending out MIDI Clock to the pedals and to Audiobus, but then Audiobus was basically sending, I guess, a parallel signal out to the pedals, doubling the tempo. Have to be very careful with your connections!
Anyway, a long-winded debriefing, but some of this may help someone! I may do a video tutorial on my set-up in the future as it is pretty interesting!