The short (and painful) answer to this is there is no way to avoid fit issues. The only true way to get a (as close to) perfectly fitted shirt (as possible) would be to have a tailor make one for you and then have subsequent fittings and adjustments made. This takes into consideration things like sleeve pitch, collar modifications, length adjustments required to remedy shrinkage, etc, etc. However, this process is not the goal (nor should it be) of a MTM shirtmaker. Let alone one that operates on the internet.
I have turned to online shirtmakers to make the majority of my casual wardrobe (OCBDs and the like). However, I only get good results by taking measurements from my pre-existing bespoke shirts and denoting every fine detail and measurement involved. Sometimes the result has been great, sometimes not so much. However, remember the nature of the beast here; it's on you to get the end-product correct, not the maker. This would be a different story if a IRL tailor were involved.
My simplest advice would be to have multiple measurements taken. Take your own and then have a tailor measure you. If you're lucky, the tailor might even offer up advice on posture or necessary corrections to your current shirt. However, this will likely not happen unless the tailor has made garments for you in the past. From there you can "average out" your two measures and go from there. As with anything, I'd also recommend ordering a test shirt (in a cheaper material and with a more simplistic design (i.e. skip all the bells as whistles so often discussed here). That way you can get a more objective idea of fit and necessary alterations.
This right here. Said much better than I did.
Only thing I'd argue different is to find a RTW shirt that fits you as well as possible and then tweak from their--add some here, subtract some there, etc. Then you know what you are getting.