Ya, the seams still join in the same place that they would if you overlapped. You are just cutting off the overlap and replacing it with an accurate cover strip. Most people will trim down past the overlap anyway as AM armor is so large.
With my AM kit, I only had to shim the bicep, thighs, and kidney / ab plate. Just about everything else got trimmed way down.
If you use the butt-joint method, your armor will fit you better anyway. You can tailor it to your body rather than the generic mould it came out of.
The best thing is to tape up a test fitting starting with the forearms and post pics before you trim. We can help you make sure you have the right idea before you start. We are glad to help!
Isaac