ps: this is just a quick idea. no idea how to implement that or what needs to be watched for in all these mods since i am no modder and also didn't use IR yet.
if/when IR already has a wood/saplings/forest cycle and you only want to use the surplus saplings to plant trees with this mod, would it be more easy and useful to create a new mod with dependencies to both mods instead of requiring one or both authors to change those mods ?
maybe, that new mod could patch trees to no longer give seeds in this mod (setting the factor for seeds per tree to 0 instead of >=1; needs checking whether that can cause a division by zero somewhere, or even directly set the factor in the mod options to a 0.0001 chance and live with getting an occasional "real" seed once per year) and introduce a new assembler (or a new recipe for vanilla assemblers) that turns saplings from the other mod into seeds from this mod ....
since the Fantario mod also has a wood production chain, maybe the same or a similar "conversion mod" could be used for Fantario seedlings as well, and/or that "conversion mod" could replace the wood chain, making wood with this mod instead of an assembler. and of course, there are even more mods with wood production chains (bobsgreenhouse, etc).