Saving TIFs in Gimp: flatten vs merge

Hello folks.
I noted in another thread not too long ago that after I worked on a photo in Gimp and then saved it as a TIF, that DPP wouldn't open it. This is what I found out this evening:
When you save a TIF in Gimp, if you have more than one layer, it gives you a choice of either flattening the layers or merging them. I don't know the difference, so I've always just chosen the default: merging. And then DPP wouldn't recognize the file. Tonight, for no reason, I decided to try flattening the layers when I saved a TIF, and DPP likes it just fine. So I tried it a bunch of times, going back and forth between merging and flattening, and the result was always the same.
So can someone tell me the ramifications on the final photo of flattening the layers versus merging the layers? (There's not a lot in Gimp docs about this.)

Thanks

When you merge the layers they keep any transparency as if merged onto clear plastic. When you flatten them any transparency is filled with white as if it's flattened onto white paper. DPP can't handle transparency but I'm surprised it doesn't just flatten the file itself; I guess that's Canon not providing proper features as usual.

ncjohn wrote in post #10680804
...So can someone tell me the ramifications on the final photo of flattening the layers versus merging the layers? (There's not a lot in Gimp docs about this.)

I'm not a GIMP user, but I know that if you flatten the layers in PS prior to exporting, the disadvantage is that you can't go back and edit any work you've done on the layers (changing saturation, opacity, etc.) - they're all "cooked" in and are now a permanent part of that image. If I have an image that I may want to come back and work on later, I'll save one copy as a .psd file before exporting/saving it as a .jpg.