Quake 3: Team Arena has the ability to create custom HUDs using text files. Extract ui/hud.txt and referenced ui/*.menu files from missionpack/pak0.pk3 to missionpack/ui folder and rename them, update names in your copy of ui/hud.txt and set cg_hudFiles cvar to your copy of ui/hud.txt. Then edit the extract .menu files for your changes. You can use vid_restart command to reload the HUD while the game is running, so you can quickly edit and reload the HUD. See achieved rfactory.org tutorials for more information on Team Arena scripted HUD.
For Quake 3 you have to change the code in code/cgame/cg_draw.c and then compile it to a QVM to change the HUD. (This is the same in vanilla and Flexible HUD mod.)
I don’t know about IoQuake III 4K mod but it says it includes my Spearmint engine. Spearmint doesn’t have all cvars as Flexible HUD mod (which was a one off mod to fulfill someones specific requests) and Spearmint ignores Q3 mod QVMs (as it doesn’t support them) so installing Flexible HUD would have no affect. So that may be why it doesn’t work but I didn’t look at the download.