Native german speaker here. When I listened to the HRE voicelines, one of them immediately stood out:
BEFEHLCHEN?
I have no idea who approved this voiceline, but no one would ever add a “-chen” to the word “Befehl” which translates to “order”. The part -chen is usually used to add some form of cute-ness when speaking about an animal. For example Hündchen, Häschen, Schweinchen. It has no place after the word “Befehl”.
Other than that I enjoy the HRE voicelines a lot.
I had to laugh so much when I heard it. I hope they keep that in the game it’s so funny and cute to me as a native speaker 
It’s actually correct. The original pronounciation in Old High German was “bevelch”:
But Germans are famously kawaii uwu ~ ?
Interesting, I guess I cannot argue with that! Still sounds super weird to me as a german speaker
Coincidentally Japanese words end with ちゃん “CHAN” with the same meaning and usage?
This is no coincidence. Japan and Germany were fated to meet by fate.
Thats not what they say though… they say “Befelchen”. Is that supposed to be a plural or something in mhd (in the sence of “Befehle!?” → “Orders!?”). As your snippet shows: The verb form is “bevelhen” (no chen sound in that, like the modern “befehlen”) and the noun would be “bevelch” (I’d even doubt that the ch is fully pronounced).
I guess they consulted people who know their stuff, but as OP states, for a modern german speaker, “Befel-chen” sounds like the -chen addition to used to indicate a smaller (or “cuter”) variant of something. That makes it sound really odd.
When the male voice says it, I understand “Befehlche”. With the female voice I’m not sure.