Pretty much. I tried it out for my FEE3 project; if you haven’t seen it already, it’s pretty ASM intensive. Using the skill system as a base buildfile, I split my buildfile in 2. The main section had all the skill system assembly (I made my edits to this stuff first so that I wouldn’t have to touch it again), tables, and text. The second part had my map, my events, and the extra assembly I was working on, which was in its own folder for convenience. I used Makehack_1 to turn FE8_Clean.gba into WIP_1.gba, assembling the first section. Then I used Makehack_2 to assemble the second portion from WIP_1 to FETD.gba, containing what I was actively working on. The second part took about 6 seconds to assemble, and I was assembling pretty often as I tried various things. If I did it for a multi-chapter project, I would eventually start moving things I no longer need to work on into part 1, which only got assembled when I needed to add text or edit tables.
EA being able to spit out a labels file is what makes this possible, so you need the most recent version of EA to do that.
You could, of course, break it up into even more parts. At the very end, I added all the portraits of FE7’s PCs as their own buildfile; which went in the very beginning, then was used as a base for the majority of the skill system, and finally the rest. It was a bit messy with names, but it worked. It does mean you have multiple roms as intermediate steps, which could be an issue if you’re keeping your entire project on a flash drive or dropbox or somewhere with limited space, but I think the shortening your average build time is definitely worth it.