The original DOOM iwads can no longer be purchased on GOG

So the actual list of changes can be found here:  doomwiki.org/wiki/Doom_Classic_Unity_port

There are all sorts of changes, but some of the main ones include:

1. The pickup sprites for the stimpack, medikit, and berserk (STIMA0, MEDIA0, PSTRA0) are modified in compliance with the Red Cross' wish that its symbol not be used in games. Initially the pill graphics from previous Doom Classic versions were reused. This was later changed in the January 9, 2020 update to a green cross.

2. New to the port is the addition of creative credits that resemble the ending credit sequence of Doom (2016), where various levels and battles are shown briefly while the camera pans around and showing the names of Nerve Software key staff. Doom and Doom II each have their own sequences, and after the montage ends, the staff credits roll will begin. Both of these are pre-rendered videos as "credits nerve.mp4".

3. The NIN logo on E4M1: Hell Beneath has been removed, presumably to avoid trademark infringement.

4. The ZWOLF* texture with Nazi iconography (Hitler portraits, swastikas, Reichsadlers, etc.) have been censored. These were initially identical to the versions that appeared in BFG Edition, but have been edited in the January 9, 2020 patch to be closer to the original textures. The BFG Edition versions of textures which had Nazi detailing were the same as undetailed versions of those wall textures. As of the patch, they have instead been restored to the original versions and then edited, replacing swastikas with the triangle logo used in the German version of Wolfenstein: The New Order, while Hitler has lost his toothbrush mustache, making him resemble the Staatmeister from the Super Nintendo version of Wolfenstein 3D. The definitions in TEXTURE1 are identical; it is the patches that have been changed.

5. The Wolfenstein SS (which were effectively removed in BFG Edition) have been restored. As of the January 9 patch, the second half of their sight sound has been redubbed - they now say "schutzkämpfer" instead of "schutzstaffel", the first half still using John Romero's voice while the other half was re-recorded by Mike Rubits of id Software. Their death sounds are as normal.

Will there be anything advantageous about this new version? For example, would it be easier to modify? I really know nothing about this situation.

This 100%

Modify engines and they will let you do it

As long as they maintain the original WAD structure and lump formats, one could theoretically have a port that binary patches only relevant pixels in affected lumps automatically. Historical accuracy then becomes yet another bullet point official ports cannot match. I guess it's not impossible the Red Cross could get pissy about it and breathe down a port author's neck if it gains attention, though.

I guess the other bits get messier, esp the NIN logo.

Do modern Quake distributions nix the NIN logos on the nail boxes?

Edit: Re hotpatching IWAD feature: would be funny to see an arbitrary color option for the crosses kind of like alternate blood color swaps. Not a request, as it'd be useless for me, but just something that came to mind.

Wow, really?  I had no idea about this!  I'm going to check on my end to verify if GOG has this.

EDIT:  I can't easily install the GOG .exe installer on Linux without jumping through a bunch of hoops, so I'll have to mess with it later.

As far as I understand GOG's system (I cannot verify it, having owned the legacy packages before), if you purchase the new bundle, you will be able to download the original installers. They are just not at the store front.

Maybe innoextract? I've used tools to extract from gog installers on win. That's what a quick search for Linux kicked up.

Per my understanding, the original IWADs will not be in GOG's installer for the new bundle.
You will still be able to download separately the original DOSBox installers (separate EXEs).

Refer to the following post:
www.gog.com/forum/doom_series/doom_1_doom_2_gog_please_include_original_dos_versions/post6

And pic:
www.gog.com/upload/forum/2024/09/987b597bfba4baed453a8d5a951cb89af392b9ca.jpg

I just downloaded and extracted the GOG release of DOOM + DOOM II.  I can now confirm that the GOG version does NOT have a "base" folder with all the original iwads.  Meaning that if you had not already purchased the original iwads from the 90's, you will not have access to them by purchasing the DOOM + DOOM II package.

Joe, are you certain that the "base" folder present in your Steam installation actually contains the old iwads?  Or are they simply the new ones with the changes?  An easy way to confirm would be to check in SLADE3 for the Medikit graphics with the green cross on them.