meudoland: by reading that post I think the GOG version is really messed up, or am I misunderstanding??
That post is correct that there was a problem with a GOG update, but exaggerates the extent.
Bengeddes did a file comparison of the GOG version and unpatched disk version to determine that they were mostly identical. The disk patch is only 10MB, though, so with a 2GB install every version is going to be mostly identical using that criteria.
The final disk version of the game was 1.0034. The first GOG release (1.004) added some bugfixes and changes, but also introduced a serious new bug. When that was fixed (1.005), somewhere during that process the programmer reverted to an earlier version of some of the code.
For bugfixes, some of the 31/32/33 fixes remained (the 34 patch only fixing a problem with 33 and removing the copy protection), and some did not. Most were rare to uncommon issues. The resurrection fix from 1.004 remains in the current version (and maybe spellbooks), but the fix for True Shot and the damage portion of Crossbow Expertise are gone, as is the switch to percentages for all the expertise skills and updates to the tooltips.
Probably the most significant loss from the disk patches was with Finnigan's magic lockpicks. In a game started in the updated disk version, you can return them to complete a quest and then buy them back, and he is a decent trader (especially for survivor type supplies). In the download version, you can not buy back the lockpicks (it was silly being able to buy them back, anyway, especially at the price of a regular lockpick) and he is not a merchant. The magic lockpicks will also disappear if dropped directly on the ground, though there is a fix for that (and given their usefulness and light weight, there is not much chance of people wanting to drop them).
When the Divinity Anthology was released, Larian had to re-do the widescreen and higher resolution support, due to several issues with backups (blog post
Hatching the Anthology). This resulted first in a Steam release (1.006), which was virtually identical to the GOG release (support was dropped for Win98 and the menu at the bottom of the screen could no longer be minimized to 3 lines for health, mana and stamina), with only one or two minor differences in bugfixes; 1.005 'fixed' scorpion traps so they were no longer overpowered, while in 1.006 they were overpowered (possibly deliberately, given how often they are recommended in walkthroughs and topics where people are having trouble), and I'm pretty sure I found another difference.
When Divinity 2 was released on GOG, DD and BD were also updated to the anthology versions.