I am curious if you are using SBT incremental builds? (putting aside how hard it can be to get and keep SBT working for a project ... I was the guy that had to do that so I know that pain quite well). Because in my experience with really large scala projects that should not be the case, unless you modify a file at the very top of the dependency tree.

We used what I would call the package object predef pattern, which basically involved, rolling your own predef to have certain functions / extension classess / objects always in scope through package objects added to each sub-project. And the build would cross-compile both jvm scala and scalajs. It would not take more than a second or two unless one of those predef files were touched (which would fire off effectively a full rebuild).