"Seems PCM conversion can actually clip even when the original source does not."
"Inter-sample overs" can produce clipping and there are DACs that know how to handle them including newer Benchmark and RME DACs. There are software players that handle various digital clipping including Roon. Roon even includes a clipping indicator. These become more important when you're experimenting with DSP settings.
See the article linked below. Roon MUSE is just the DSP engine which is part of Roon. You can choose to use various MUSE feature - or not. Headroom Management is one feature that can be enabled and can be especially helpful when using some DSP settings. While MUSE is part of Roon the article is helpful in understanding clipping in general.
