They still release harmful particulates, they still release lots of NOx
Frankly, those are just local problems and thus negligible (compared to greenhouse gas emissions).
they are doubly bad in terms of land utilization, where you use huge swaths of land to cultivate plants with the sole goal of making them into fuel, rather than using that land to make food. Moreover, in a lot of places the cultivation of biofuel plants is being done by burning down forests and using that land for farming.
So don't be stupid about it: make as much of them as you can out of waste fats and oils, then stop. Easy-peasy!
I'd also argue that if we 100% switched to biofuels we'd have massive issues in terms of land, farming-related emissions, deforesting etc.
This isn't wrong, but it's a massive strawman argument because doing that would be idiotic anyway. Biofuels are best used for filling the gaps left over after cities are fixed for bikeability and everything reasonable to electrify is electrified. (In other words, they're the answer to "but what about my [insert special-snowflake reason why I can't ride a damn bike/train/electric car]?" pearl-clutching.)
There is no one solution to sustainability, and pretending there is is a fallacy.
Only if you're stupid about it and overuse them. My diesel VW runs on 100% biodiesel made from waste fat from chicken processing that would've gotten landfilled or something otherwise.