Binary hacking edits a rom. Decomp hacking builds a brand new rom.
There is no practical way that decomp hacking uses binary hacking. The only way that's possible would be compiling a pokeemerald rom and then using a HexManiacAdvance (you mentioned a large amount of binary tools, but for the record HMA has replaced all of them. It's better and safer to edit roms with and should be the only binary hacking you're using) to edit it, which is redundant. Any edits you want to make should be done in the decomp because binary tools generally won't know where to do their edits once your rom has been edited in the decomp. HMA can figure things out, but still
Binary hacking rarely ever uses the decomps in general hacks. HexManiacAdvance already does everything needed to make a full-scale rom hack like Pokemon Gaia, and there's little need to even reference the decomps. Sometimes you may want to use the decomp syms just to find an offset that isn't recorded in HMA yet, or find out how and where certain things are used in the game, but even that's rare nowadays.
Binary hacking can use the decomps a lot if you're doing very advanced things. Occasionally I will take a look at the decomps to see how certain functions work to help me edit the ASM code, or even compile a new rom and transfer over the code avoiding the need for a C-injection. But I do that rarely. If you'll need to do a lot of function changes, you might as well just make a decomp hack.
Basically outside of a binary hacker using the decomps for research, there's very little practical overlap.
I always recommend you pick one based specifically on your goals. If you're going to edit a lot engine functions and change the base game, you're probably going to want to use the decomps. Especially if you're fine with programming. Binary hacking comes with a lot of limits in that you can only edit the peripherals of the game - pokemon, trainers, maps, story, etc. Apart from the CFRU ofc. Plus you can label anything and use source control.
On the other hand if you only want to edit the game itself and keep the Gen3 engine mostly the same, you might find the decomps are a bit overkill. For example just replacing a pokemon is an absolute pain in the decomps with the amount of files needing to be changed, but in HexManiacAdvance it's a few simple clicks.
Mapping and scripting a story are basically the same in both now thanks to HMA replacing Amap and XSE.
You're going to be stuck with whichever you pick for a project, so it's worth putting thought into it
EDIT: I guess I should mention that while it has nothing to do with the decomps themselves, the CFRU is basically a tandem of using a codebase to edit the game and also using binary hacking tools on the rom. That might be the workflow you're looking for
