damjancd the only thing you can do to not fry eggs with your iphone, is that you need to limit the everytick checks of the webgl, and use it only when its needed... unless u have some webgl dependent effect which must stay always on, then ur pretty much... footless as you said.
as referring to compiling the best, i find intelxdk the best wrapper atm, its self explainable, no big things to understand to just "poop" c2 apps with it.
i dont know how you find yourself in this type of situations with compilers ... its like 1000th post complaining about compiler software that are doing "something wrong" to the .apk or .ios format.
never encountered any issues so far, the only issues i seen in my past projects, was that the projects where all messed up(unoptimized/bad event sheet coding) from beginning not the compilation process.
most people are co-dependent on function calls, while i get it its useful, its very cpu intensive when run'd in 100 loops or very fast conditions to almost everytick conditions.
also, you read the latest update? im guessing didn't applied in January, but now Ashley enabled 2 versions of webgl, so your app i think should work better, if you are re-exporting.
but then again, depends on the iphone ur testing the app with, early ios devices(before ios7 or 8 cant recall) dont support webgl, so its a big market issue with iphones there.
good luck, and hope i see ur game in the top charts soon, i love the graphics u made, they are amazing.
P.S the only compiler that i encountered issues with was the ludei one when they released in beginning in 2014 -2015 but then i switched to intelxdk and never had any compiler problems. never used phonegap mainly cause of their free app license