it fixes only the model issues that were also in ioq3 version. I don't honestly know whats going on with rend2 rendering right now... (There is a fix for not requiring r_floatLightmap in ioq3 tree now too, but I'm not too concerned about that yet)
If they're named something alphabetically before assets, they'll not even be used if the internal filename you use is attempting to override a base file.
That just looks like your config was set incorrectly at one point like those cvars had a floating point in the value or something. Unexpected end of info file isn't really a uix86 end of file. It means you have a bad arena or bot file.
They don't count towards the server side entity limit, cgame only. But they have a cap. And count as refent's so that can hit the 2048 limit and they don't really have lod or anything like that. So PVS differences and different FOV can cause them to disappear (_static).
If you have vote enabled on your server in JA+ or any other mod thats older (not based on improvements from mod_base or OpenJK/JA++), then you should probably be using sv_filterCommands 1 with OpenJK. You lose out on ability to have ; in your chat, but it protects against an exploit in callvote which allows them to change settings on your server. It's off by default due to the fact that it blocks ; usage and that its fixed in modern gamecode.
You gotta make sure the engine and renderer are in sync. Doesn't appear to be any changes at first glance but there does seem to be some sort of issue. Release and Release helps too.
I'm not sure if theres an easy public link to OJP's source code anymore. And no, its not technically compatible with any OS other than what it was ever released for (probably only windows-32, and maybe mac (universal?), and a linux-32 server)
Config size should not be an issue anymore, the 3 configs attempted to execute on startup used to share a single much smaller buffer. Now they can all be ~128K each.
On topic of the original issue: They're just injecting custom information for getinfo requests of said IPs of the servers in question. The cause of the changing of lines is a control character of the likes of 0xB. As @@Xycaleth said, its pretty easily fixable but we just have ignored it for the time being as its not a huge issue because its not exploitable on a large scale to affect others' servers without access. OpenJK does not exist to play cat-and-mouse with TnG. We simply want a fixed version of the game. If TnG chooses to make exploits that become known or reveal ones that had eluded us previously we will investigate but only on the basis to attempt fixing the game not any sort of attack against TnG.