You are confusing nikgapps with flamegapps. With flamegapps basic the dialer is not replaced. With this ROM, flamegapps is recommended.
You can also flash full flamegapps and select what you want. Just download the txt file from here: https://sourceforge.net/projects/flamegapps/files/arm64/gapps-config/
Place it in the same directory where you have the flamegapps zip file on your phone and edit it and replace the 1 with 0 to skip a component. The txt file must be in that same directory on your phone storage when flashing from orangefox. Note that by default the camera app is removed on flamegapps, be it basic or full variant, but there is also a setting on that file if you want to keep it.
Then if you already are in this ROM and just want to have flamegapps costumized or replace nikgapp, redownload the ROM zip file from GitHub (see first post) and put it on your phone, then go to orangefox and:
- wipe system, caches and vendor (keep data intact, as you were already on this ROM)
- flash the ROM zip file
- flash the flamegapps zip file, full or basic (don't forget you must have that txt file on the same folder if you want to customize it, mandatory if you are flashing full flamegapps and want to keep stock dialer)
- wipe caches again (won't hurt) and reboot to system at least once (everything should be okay)
- if you need to flash magisk or other stuff, only do it after that reboot
This has worked fine for me everytime I wanted to change stuff in flamegapps without losing data or internal storage. But in doubt, make a backup from orangefox to SD card if you want to be extra safe.
And btw, thanks @zeelog and @anandsvm - with the new option I can now use the stock dialer to always record calls (even though there still is no option to manually record... but I know it's not your fault). You guys are awesome.