All the biomes where RC adds his trees prevents Terraqueous and HarvestCraft trees to spawn, mainly forest biomes.

That's sort of to be expected. The tree replacement system in Forge is really basic, and unless those mods spawn them in not as trees but as structures, there is no way to do both. I'm still waiting on MinecraftForge/MinecraftForge#3318 to be pulled to fix some of those issues.

For now you can use the biomeGenerationMatcher to disable ReC trees in specific biomes if you need different ones to spawn, or you can export those trees as ReC structures and weigh them in again using the ReC spawning system.

The menril trees from Integrated Dynamics don't spawn neither.

So why not generate your trees as structures ? It would solve all the problems.

Because I want to replace vanilla trees with this system. If I were to simply add mine, it would quickly result in too many trees.

Plus, the biome should be the information point in determining how many trees a chunk contains, as that information is already provided. Structures would have to set up the values from scratch.

(edit: you can, of course, edit the trees to spawn them in as natural structures rather than decoration replacements, solving the problem for yourself)