I've got this game on DVD-ROM. I couldn't say for sure what the difference between my version and the CD-ROM is, but the DVD-ROM has about 800MB of important-looking data on it (not counting clearly vestigial stuff like QuickTime and Acrobat in 20 different languages for both PC and Mac), which is more than you can fit on a CD, and more than GoG's 415MB. My guess is that the DVD version has better quality FMVs.
Also, I found that the DVD-ROM version works great on WinXP if you install Quicktime Alternative, specifically version 2.6.2. Anything newer, including Apple's version, causes problems.

I might speculate that this is how GOG has gotten around the compatibility issues with newer versions of quicktime. Perhaps they've modified the original file formats to something newer and with better quality compression.
My take on the original CD vs DVD (I think that was just for Riven, wasn't it?) was that the CD version came on multiple discs, but the DVD took only one.

Riven CD had five discs, but Myst ME only had one.
Searching the DVD-ROM, there are exactly 799 .MOV files on the disc (not counting the "Making Of" videos. In total, they weigh 597 MB. In addition to those, there are also these large files:
\MYST.DAT - 70.6MB
\SELEN.DAT - 66.3 MB
\STONE.DAT - 66.2 MB
\CHANNEL.DAT - 60.8 MB
\CD Data\MYpics - 35.2 MB
\CD Data\CHpics - 33.8MB
\MECHAN.DAT - 31.5 MB
\CD Data\STpics - 17.3 MB
\CD Data\MEPics - 13.5 MB
\CD Data\SEPics - 13.0 MB
I tried taking those 10 files - just those 10, and compressing them using 7z. The final compressed size was 289 MB. If GoG's version includes those files compressed, that only leaves 126 MB for the FMVs, which isn't much considering my version's FMVs are nearly 600 MB.
Maybe someone who has the game could help me out? If you can, open up a command prompt and CD into the root of the game directory. Then type this command:
dir /S > myst.txt
Then there should be a file in the directory called "myst.txt." If you could upload this text file somewhere and post it, I will analyze it and how it differs from my disc's structure, and possibly find out what GoG had to cut to make the game fit in 415MB.

I still wouldn't doubt that if they replaced .MOV with some other format they could get it down to that size. Those original .MOV files were probably raw and uncompressed, or barely compressed by today's standards.
It's not unthinkable that they could be re-encoded with WMV or OGG or H.264 or something at a 5:1 compression ratio and very little quality loss.
It doesn't seem like GOG would cut anything out of the game. That would be very out of character, but I hope someone posts that directory file because I'm very curious about how they managed to get it so small and get around the compatibility problems with quicktime. It seems like replacing the video codec would be a serious re-engineer of the software, but it's probably not impossible with cooperation from the owners.

The single biggest MOV file is "SPAGE5.MOV." It's the movie that plays when you bring Sirrus the fifth page and he tells you where to find the green book. It's 4:20 long, and weighs 22 MB, so it is certainly not raw or uncompressed, and it's just not going to be possible to compress it even further to the point where 800 MB fits in 126 MB without seriously compromising video quality.

DVD-ROM or CD Version, I'm not sure, but considering it seems to be working with the most recent version of Apple's Quicktime (not qt alternate) and the recent version of iTunes on my Vista-64bit laptop, I'd bet they made some changes to the original MystMasterpiece movie files..... I will agree... it doesn't seem as crisp as I remember Myst Masterpiece from my 10year anniversary edition, and the sound seems a bit more fuzzy (but that may just be the fallibility of my memory. I will need to check it against my installed copy of Masterpiece at my home computer (that's not running iTunes, so it still works)..... will report my findings later.