As far as I know, FRAF is the only way that fanworks have been/can be monetized. If you attempt to monetize fanwork of what is technically someone else's "intellectual property", then the copyright holder can demand takedown or pursue legal action. The fact that fans and bootleggers have been doing this mostly without interference does not necessarily mean that it is safe to do so; think about it as similar to Nintendo's behavior, where fan projects working in the open for years, even non-monetized ones, are suddenly met with aggressive litigious action.

This could apply to anything that could reasonably be traced back to Homestuck; classpects, species, characters, settings. If you don't make a splash, you might not get noticed, but the larger you get and the more money you get from what you do, the more likely that action may be taken against you.

I am not a lawyer, and anyone can feel free to correct me on these points, but unless the licensing for Homestuck changes in a way more substantial than a few handpicked fan projects getting the OK when they declare it so, it will always be a serious risk to attempt to monetize a fan project, even if you use zero original comic assets in there.

By contrast, Touhou's creator, ZUN, has a license for the Touhou franchise that allows creators to make games with full leisure of the characters, setting, and concepts of Touhou's world. This has led to a flourishing ecosystem of fangames that have enriched the fandom as a whole and led to its enduring popularity. It might be possible for Homestuck to alter its license in such a way, but this would require a complete rethinking of the peculiar philosophy of brand management that Homestuck is currently run under.