The same original UT99 Goty discs were still used to install the Linux version but there was a Linux installer that you could use to install them. Some years back when I did this, it required some old libraries to get the Linux installer to run.
You definitely want to run v469 for native Linux though it was a vast improvement even at v469a. So just follow the instructions from the patches link that Ooper posted to do native Linux if you want to go that route. It basically has you copy the files you need from the install disc(s) to your installation directory where you have extracted the v469 patch files.
If you just want to get the wine install working with ACE you just have to make sure you are using a wine version that is compatible. I can't say all versions of wine that ACE allows but I can tell you that I successfully used wine v4.17 (staging). My guess is any wine version 4 would work and was probably the latest version of wine when ACE v1.2 was released. If you get kicked because of kernel32.dll and/or msvcrt.dll it is most likely an incompatible wine version.
There are a few players using wine successfully on the London combo server if they see this post it would be nice if they could post their wine versions. Typing wine --version at a command prompt will print the version number 🙂