Issue: When using the cobblemon mod, this mod overwrites rightclick behaviors (held items and shoulder mounting).
Possible Solution: blacklist mod interaction with cobblemon entities or add a config to enable on to do so.

You can already change the shift-rightclick behavior to require a held item (so it'll use Cobblemon's shift-rightclick by default), or block the mobs completely in the config.
The latter will disable all features, including idependence.
Just set the required held item to one you're always holding, like your main weapon.

I'm not sure how much sense a separate interact-blocklist would make, since whistling always targets groups of pets.
Maybe I could rework whistling to target specific mobs under your cursor, maybe...

Just released new versions with a separate Interact hotkey (H) and a sneak interact blocklist afterall, containing cobblemon by default.

The "sneak interact while holding a specific item" way I mentioned still works too of course (just don't forget to remove cobblemon from the blocklist).