I struggled with this too! After only just beating it, vfqd told me about a strategy that makes it significantly easier. I don't want to spoil it for you if you want to figure it out for yourself though!
Please do tell, I have absolutely no interest in slamming my head against this wall anymore.
You only need a small piece of fynbos to start a fire, so if you plan your excavators so that they either just cut off one tree, or that a tree creates fynbos across a river, you can use that little piece as a firestarter for forests while keeping all of the rest of the fynbos for biodiversity.
This way you're not using up the existing trees for forests, and any new trees that you get from the Arboretum can also potentially be used for beehives.
Another possible approach I've found to work is to leave unscrubbed wasteland around the edge of the tiles that will become forest, then build new scrubbers/greenhouses on the margin around the forest after the placing the arboretums. You need to plan ahead a little to make sure you can actually get power to those parts but otherwise its quite simple and can give quite a lot of tiles for fynbos.