Silgrad, for example, places a boat outside the Tax & Excise Office, which is sitting inside the boat you arrive in. It also adds a chest next to the barrel with Fargoth's ring with three items that don't have textures or icons. When I tried one on, Morrowind crashed. I expected a crash but since I was testing this out, I had to know for sure. It also overrides the local rumors about Addamasartus and the murdered tax collector. I also think this conflicts with the Seyda Neen transport mod for Tamriel rebuilt, which also places transportation there.
He also suggests Seyda Neen docks. I'm not going to lie, I like this mod, although it appears to be half-finished. Several houses are in the water, and it looks like there's supposed to be wooden pathways connecting them, as well as the stairs up to the transport boat, but they're mostly not present in the village itself. It also appears to add a couple of trees and at least one building between the lighthouse and Fargoth's hiding spot. Since this is an early quest a new player is likely to come across, this will probably make completing it an exercise in frustration.
I already made http://www.gamesas.com/index.php?/topic/1097800-ice-bradys-robes/ about how he links to a Russian translation of Canadian Ice's robes. He suggests Better Clothes, but the Russian translation overwrites all the references so that the clothing is named in Russian and uses the original textures.
When he suggests not installing the official Bethesda mods, he states that the Master Index plugin actually overwrites the improved orc heads installed in another mod, but this is not actually true as far as I can tell.
I suspected there'd be a lot of conflicts and weirdness, and I already had several other mods I wanted to install that would conflict with his suggestions, but after running into trouble with the robe mod, I checked a few others out.
I think he's collected a lot of really good resources that improve Morrowind's appearance, but I think he's assembled more of his favorite quest mods more than simply mods that enhance a new players experience. Am I wrong?