Welcome to lossy compression… The de-compressed data is not identical to the original. 
M4A is lossy. FLAC is lossless. The “best” compression means it’s working harder and taking longer to get more compression (a smaller file) but FLAC is always lossless (unless you change the sample rate of bit depth).
It should have less effect on the loudness (RMS or LUFS) than on the peaks.
The same thing happens with MP3, but often the peaks get higher. Probably most of my MP3s ripped from CD go a little over 0dB “show red” for (potential) clipping in Audacity. (The original CD audio can be clipped at 0dB but it can’t go over.)