True Sight is still broken in the download version, and I think spell books ignore level requirements.
The problem with encumbrance was that if you placed items in a container in your inventory the weight was not updated right away, but only when you moved or changed something directly in your inventory. Since nothing can be placed in the inventory if you are over your weight capacity, if the action that triggers the update was something that would normally result in an item being put in your inventory (like drag and dropping an item from your inventory to somewhere it can not be dropped, or clicking on equipment in your inventory to swap it out with your existing equipment) that item would be destroyed. I think that is still the case in the download version, but if you save before moving a bunch of stuff around this way, it would be easy to recover from if you do have a problem.
If you don't need higher resolution support, then the disk version has a slightly smaller chance of running into some rare bugs than the download version, and there is a relatively rare bug (with an easy fix) specific to the download version.
For actual gameplay, there is a quest in Verdistis to steal back a very useful item that the city guards impounded; in the disk version you can return the item to complete the quest and then cheaply buy it back (which is nice, but not very realistic), while in the download version you can not buy it back, so need to leave the quest unfinished to keep the item (though that is an easy trade-off IMNSHO). The quest giver is also a decent trader in the disk version of the game, but not download.
With the disk version of the game there is a configuration file edit to skip the intro videos (see
here), which you may want to do after you have seen them at least once.
In the patched game (1.0034) this will also eliminate the need for the Play CD, except for a couple cases (a ceremony you trigger late in the game, and at the end of the game). These are the same limitations as with the no-CD hack.