Pheace: I think the biggest concern is that it might not allow you to download the *installers* but rather only the 'preinstalled' versions.
On top of that I guess there might be a worry that there will only be a 'Galaxy ready' installer of the most current version of the game, rather than having a base installer for the game with patches (so you can choose which patch you want to be on). Not sure how that works with the newer games GOG already has though.
Has GOG said yet in which "format" the default Galaxy installations will be? The two options I see are:
1. The Steam way: there are no separate installers (nor patches), the download and install procedures are seamless with the client, as well as (auto)update. In this case yes, it is a relevant question about the standalone installers (and patches), how they will be managed.
I don't necessarily consider this optimal from GOG point of view either, as then they would have to maintain two different formats for their games: the one which the client uses, and the standalone installers. If this was the case, I am not expecting the client to support the standalone installers, they will be handled differently. Maybe even offering a mere http download option for them, similar how e.g. DotEmu does it.
I also think it would be probable in this case that there wouldn't be separate standalone patches anymore, but only a installer which is kept up to date. I personally would be fine with that (especially as quite often the standalone GOG update installers don't work with all previous versions, so quite often you end up reinstalling the whole game anyway).
2. The "Humble Bundle Android client"-way: as far as I can tell, this HB client downloads the normal .apk installers, and then installs them. You can also access and install those same .apk installers manually, ie. using the client only as an installer downloader.
Not sure if there are similar clients for Windows too (e.g. Desura? Never used it.), but this way GOG would have to maintain only one format that covers both the needs of the client, and the people who want to keep standalone installers (and possibly patches).
However, this could also be a bit clunkier/slower, and mean bigger downloads for updates, at least in those cases where you have so old version of the base game that the new patch is incompatible with it, and the whole game needs to be re-downloaded and reinstalled.
Or alternatively, GOG would finally be able to offer update installers that always work with all previous versions of the game installation, something that hasn't been always the case so far AFAIK.