The way I have been doing it for a while is as follows:
1. Use Toleda's cloverALC script. This places .zml files inside AppleHDA.kext. It places patches into Clover config.plist. It installs realtekALC.kext into Clover kexts.
2. I grab an unmodified DummyHDA.kext. I take the .zml files out of AppleHDA.kext and put them into DummyHDA.kext. I take realtekALC.kext out of Clover kexts. I take some info from the Info.plist from realtekALC.kext and add it to DummyHDA.kext. I leave the Clover edits as it.
3. Put DummyHDA.kext into /S/L/E which leaves AppleHDA.kext vanilla.
4. Often I have to rebuild the kextcache to get DummyHDA.kext recognized.
If I have a new installation, I can just put DummyHDA.kext into /S/L/E and copy my patched config.plist to Clover.
An advantage is this: on some computers, mostly laptops, sound gets unloaded during sleep. In order to reload the kext after sleep, it needs the enabler. With realtekALC.kext in Clover, it only gets injected at boot. It is not available if AppleHDA.kext needs to be reloaded. The DummyHDA.kext has an alias to the AppleHDA.kext binary.