Call me a fool because I am! I must have forgot to activate QPel and GMC on the sample I encoded with Avidemux or something because I'm testing again now, and everything seems to be as it should be; second pass noticeably slower!?! Yes, I tested only once before, and sloppily. Is a different arrangement of switches in Avidemux' GUI enough to confuse me to the point that I forget to activate some switches or did I press cancel instead of OK after modifying settings? Anyway, bloody stupid of me. Forget it and paint whiskers on me while I sleep.
I'm very sorry indeed for the unnecesary call for improvements there.
P.S. SadaraX, I meant an RPM for the all-in-one-MKV-application you mentioned.