So far I could not reproduce the error with Bioluminescence, but I also heard from friends that it existed for a short time. This confuses me a little. ^^'
If it occurs again; What additional mods to HMM do you use? What are your basic-Factorio-settings in graphics?
About AAI-Vehicles: You can either click on such a vehicle and then select the remote in the upper left corner (again for the other one) or use the corresponding hotkey ("Z" in my controlls so far despite multiple assignments). Because of these possibilities I deactivated the recipe and item by default, which also has other advantages, but if you deactivate "HMM: Settings - hidden" you can undo that.
HD-Mods: Yes, you can simply deactivate them if they are too annoying for you. I do that sometimes too. xD
I'm currently working on a lighter version of the modpack, which will work without the HD mods by default and will require some more resource-efficient settings. Bioluminescence for example would be dropped completely, due to it's huge impact on the UPS and only limited necessary features. ^^