I figured out the problem a long time ago. Since I just had to go through this again, and this came up when I searched for this issue, this is what I did...
The problem back then was that the P99 folder I was using (from Windows) had dgVooDoo2 in it, so it had additional DLLs. Attempting to start the game up just blipped a blank window for a split second and then disappeared. Messing with eqclient.ini didn't help. Changing 64/32 bit in Bottles doesn't matter. Removing the dgVooDoo2 proxy DLLs is what fixed it. Specifically, these DLLs: D3D8.dll, D3D9.dll, D3DImm.dll, DDraw.dll. I'm not certain if all need to be removed or just one or what, but moving them all out fixed the problem for me.
Since then, I have given up on Bottles, and now I just run it through Steam (still on Bazzite). Go into Steam > Add game > Add a non-steam game > Browse to eqgame.exe. This is how I have it configured:
Alright well you can't paste images into this old ass phpBB.
Shortcut
Target: /home/foo/p99/eqgame.exe patchme
Start In: /home/foo/p99
Launch Options: [blank]
Enable overlay: off
Include in VR: off
Compatibility
Force use of specific tool: [checked]
Proton 10.0-4
Controller (unchanged?)
Override: Use default settings
Use Desktop Configuration: [on]
Game Recording (unchanged?)
disabled
Customization (unchanged?)
all defaults
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