I have two answers. A quick answer and a long answer.
First the quick answer.
They are from the same tree (MPEG-4) but from different parts of that tree. So, essentially the same but different.
Which is better? That depends on how you tweak their respective settings.
Now the long answer.
MPEG-4 is a collection of standards (or methods) that define the compression of a/v data. So it's like going into a car showroom and being presented with a list of all the different cars the showroom have. MPEG-4 being the car showroom and the different cars being the standards for compression.
Software/hardware developers pick from the list of MPEG-4 standards and feature sets to develop their own applications that compress and decompress a/v data. Their choices are made based on their own particular requirements.
Microsoft's flavour of an MPEG-4 codec is contained in the .avi file format, simply as a branding exercise. They already have their own file format a/v wrappers (.avi, .wmv, etc) so they decided to take from the benefits of the MPEG-4 feature set and stick it in their own file format.
SpeedEdit utilises one of the MPEG-4 standards (also known as Parts. Part 12 in this case) that pertains to file formats, this being .mp4 the file format. So they've taken their pick from the MPEG-4 feature set to develop their codec, then contained it all in Part 12 of the MPEG-4 standards list, that being the .mp4 file format.
So, which codec is the better one? Well, it really depends on your needs as an editor. Where will your project be seen? How will it be distributed? How compatitble does it need to be? Etc, etc, etc.
The beautiful thing about the MPEG-4 standard is, that whichever flavour of it you use, you can more or less guarantee it can be played back without any issues.
Ofcourse, this is an over-simplification, since the whole MPEG-4 thing is a LOT more indepth, containing stuff like, profiles, levels, subsets, etc, but in that's the crux in a nutshell.
Why would you choose one company's flavour over another company's flavour of MPEG-4? Well, that I don't know. Maybe one of the other's can help with that.
Hope this helps.