Generally inferior, yes -- and often by quite a bit.
MainConcept has their own standalone version (Reference), with many tweaks available to encoding parameters. And then they have an SDK (software developer kit) version, used by software developers like
Adobe, Sony Pictures, Ulead/
Corel, and others. How feature-rich or stripped it is depends on the limits of the SDK license, as well as the choices of the software makers.
Adobe Premiere CS4 was really the first version of the
MainConcept SDK that was pretty feature-rich, and could be customized quite a bit. I've been using MainConcept since the earliest versions, both as standalone and in Premiere.
Most problems are due to picking a template, like "DVD", instead of manually selecting all desired options, for achieving maximum quality. Quality is really based on settings customized for you video content, length, source, and output needs.
I stepped a buddy through MPEG encoding in Premiere CS4 several months ago, and it took about an hour to teach him. (Honestly, he'd probably fail a test, too, if I gave him one. He mostly just wanted me to hold his hand. Not that I blame him too much -- it was for a one-off project, and he was stuck using a lab/studio that was not his own.)
When it comes to video encoders, you get what you pay for.
Some areas of videography have many free/cheap tools, and are known to do an outstanding job. But this isn't one of those areas.
