I remember as a kid playing Twinsen's Odyssey with the Windows version. I see that there is a windows .exe file, but It doesn't run the game. The Windows version had better gamepad support. Is there anyway to implement the Windows version of this game, I like to avoid dosbox whenever I can.

The short answer is not necessarily, but...
The LBA2 windows file requires specific versions of 2 .dll files to run at all. What you can do is, copy/change the LBA2.GOG file to LBA2.BIN and change LBA2.DAT to LBA2.CUE, and if you mount this with a disk image program you can do a fresh install so that you can get the specific versions of the 2 .dll files you need to run the game, smackw32.dll and mss32.dll. But after that there's 2 issues. One is that I have never gotten the game to run well on modern Windows, but your mileage may vary. And two, is that the game has copy protection so even with an image mounted, it will ask you to insert the original game CD in the CD drive.

I can't remember specifics but there's a whole community around these two games, search for a website called The Magic Ball Network. There's some fan generated content and I think a list of patches you may need. I remember playing the second game easily on Windows XP but I haven't tried playing in the last 5 years at least.