Yes, I merged them via mod compendium. Same game version. No, I dont get this warning about legacy patch. Just
! patch_log: Loading patch config file C:/rpcs3/config/patch_config.yml

I removed old patch.yml from root directory and place new patch.yml in /patches

I use exactly the same mods.
Did you enable bustup mod v3 and mod support in rpcs3 patch manager?
Manage->Game patches

I copypasted some code from rexis patch and it worked