The Classic Protocol Extension system is quite flexible (it's been expanded at least 37 times). While whatever features you introduce probably won't be accepted upstream, you can absolutely make a client that works on both normal ClassiCube and your custom modified version. Spec out a non-standard extension. When players connect to a FPS server, they get kicked if they don't declare support for it. Alternatively, you can gracefully fall back to simpler behavior when a player doesn't support your magic features.
With non-standard extensions I made (none of which went anywhere, sorry), I always prefixed them so they'd never clash with the standard, much like HTTP Headers. Something like "X-classi3-InfiniteMap" wouldn't conflict with the standard, and wouldn't conflict with other non-standard extensions made for other servers.
All this being said, modding ClassiCube into what is essentially a different game, with it's own separate and custom client, and then using the main classicube.net server index to announce and play it, doesn't feel particularly in line with the soul of the game.
Many players will try to join, realize you need an extra download, and feel like they're missing out. Won't help that most chromies are literally incapable of installing a custom client. At some point, there's no reason to keep using the old and crunchy network protocol, since you won't be interoperating with the main client anyway.
If for some reason, you still want to go forward, I feel you'd get better results forking this into a separate project, maybe it's own dedicated server list. You can still announce your servers on the main index. Although, it would be best if you kept them off the public list and instead linked to the server IDs on your own index/website instead. That way players with CC accounts can join your server.
Further down that path is becoming your own player and server tracker. Several CC servers accept players from BetaCraft, which uses Mojang accounts instead of ClassiCube accounts. This leaves the door for still allowing users from CC to join through private server IDs without having to register on your service. ClassiCube also has an OAuth system (which is used for this forum!) that you could potentially use to allow quick sign-in without forcing players to re-register for the new one. Ask AndrewPH about it, if and when you're serious about doing something like that.
TLDR: You're making a completely new game. There are many options, if you decide to use ClassiCube as the basis for your project. Doing any of them is a large amount of work and dedication, just to stay connected to the community in some way. At some point, you're better off writing your game from scratch.
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