As it is now, playing this wad in Gzdoom ruins the experience in quite a few ways. Minor things that don't work right here and there add up making for quite a few things. Of course this is expected with a Legacy wad being played in a Zdoom port.
Graf, if you want, I can try to list the things I personally have found that are different from Legacy.
-The known issue is with dynamic lights slowing down anyones computer in Gzdoom. There are a lot of special effects that would be a shame to play without. They of course are just visual, but a large aspect of this level set is visuals.
-Various things spawn in the air and fall into place. Where in Legacy it seems the spawn directly on the ground. You can notice this at the alter where you find the first teleport scroll, when you pick it up, all four corners light up. In Gzdoom, it has the effect of the flames falling from above into place. Dunno if it's actually a bug though.
Edit:
Okay, I try to explain some of what I found. I'll post in a spoiler tag, since it 'could' be a spoiler to some people. Also, some of these 'bugs' might just be my computer, so who knows. Anyway, if it's useful or not, it's here.
Don't mind the image quality, I didn't spend much time on the editing, and I made them small so I could use my own webspace. Not like you can't see what I'm trying to point out anyway.
[spoiler]
First off, the reason for the slowdown at the start is a large number of dynamic light particle effects. One of the biggest drains is a telportal effect which you can't see at the start because of a black mid texture, but is still rendered. You get to see it if you choose the Myst style of play. Not a bug, but thought I would post it to point out what you could be missing by not using dynamic lights. There are lots of well used light-particle effects used throughout the levels.
These two may be related to each other. In the first picture, is an item that you take, but in Gzdoom it doesn't display as actually being taken (the thing on the small alter with the blue energy around it).
The second image is of the effect of statues turning into monsters. As it works in Gzdoom is that the monsters spawn and drop onto the statues, and since the statues aren't supposed to be there anymore, the monsters are stuck. This appears in quite a few places. Also different types of this 'bug' appear.
Another example of the previous 'bug'. The doorway opens in a cutscene, and the blue key only stays in it's spot during the cutscene. It dissapears before the cutscene is over, but in Gzdoom it doesn't dissapear at all.
Also, the pools of water look different. Might just be a map error or something. In Gzdoom, this water pool isn't transparent, while in Legacy it is. Although, other pools of water in Gzdoom look as they don in Legacy, so I don't know.
This one should be obvious as to what's wrong. If not, the transparent middle textures in legacy are solid black in Gzdoom.
Also in this area of the map, at one point a group of lost-soul/spirit monster teleport in and are supposed to dissapear when you close the box. In Gzdoom, they aren't being removed. Pobably related to some of the above bugs.
A nice light brown fog effect in Legacy turns into just a dark cave in Gzdoom. I didn't notice that there was fog at all until I played the map in Legacy.
After you run up those steps to grap a supercharge, a cutscene raises some stairs, and puts a voodoo doll here. I didn't try shooting it though, so I don't know if it was really a voodoo doll. You have to noclip else you're stuck there.
Another bug shortly after this point, the stairs that raise lead to a bfg which triggers a cut-scene (and also opens up another area) when picked up. In Gzdoom, this didn't trigger, and stops you from going to the next level.[/spoiler]
There might be more, but I couldn't go to any of the hub levels since the script is broken there.
I don't think that they are supposed to look like that! Nevertheless, "Phobia" is one of the greatest releases for Doom ever!