Having actually distributed a mod as a standalone game for quite a long time, I can fully say with confidence that it's a bad idea. As a quick sum-up: Apocalyptic Dawn was released as a full standalone mod all the way up to version 2.4, and only the (beta) 2.5 and the yet to come version 3 will move away from that path, with the next version to be an addon that will no longer attempt to modify the menu model, etc).
Firstly, it's incredibly difficult to maintain the versions. If your compiled version of the engine had a bug, and a fix was released, you have to reupload everything. You also have to release both Windows and Linux versions, which means you would have to compile for each, and if using installers, you'd also have to compile those installers, and finally upload them online. Since bugs crop up regularly and most new versions of engines include bug fixes of one kind or another, you pretty much have to keep updating this standalone mod, too.
Secondly, if you decide to modify the source code in any way, you must upload and maintain that source code online (as per the GPL), and with each new version of your engine, you'd have to apply the changes and if any conflict with yours, it becomes more of a hassle to fix.
Additionally, the file size becomes much larger. People have to download a large number of extra files (eg, tilesets which may already be included with the engine), causing the download to be larger (not to mention more to upload). Plus, pretty much everyone who tries your mod probably has installed at least one of the Glest engines on their computer, effectively making duplicates. There's no real way to prevent those duplicates, since overwriting the main menu model would take effect for all mods installed, and could cause conflicts.
All in all, standalone releases are a bad idea. Having been one of the first to create and distribute a full conversion mod (a choice I ultimately regretted), I know how tempting it is to replace everything from the logo to showing off an impressively unique main menu model, but it just doesn't work so well with the players, and maintaining it is unnecessarily difficult.