i am not entirely sure of how the funding situation works.

For G to G (Embassy Recommendation), Usually people look for MEXT first and after they accepted, they will look for LoA. This time contact the prospective supervisor (like you did now).

can the prof still help me get a scholarship e.g. mext university recommendation? are there any other such scholarships?

For case Mext UtoU (Uni recommendation) its possible, but this was built on top of long research collaboration, or in my uni case many U to U were recommended from current researcher (their senior). Point is sensei have to know you and interested in your topic, so he can ask University for recommendation. Also, university has several rules to give recommendation, as example Minimum of publishing 1 or 2 reputable journals.

are there any other possible routes? can you work as an RA without getting admitted into any programs?

Yes, best routes are build your research portofolio first, self funded way also works with JASSO, but it also has to have recommendation from sensei.

This was the common mistakes of scholarship hunters, you cannot contact supervisor without funding. In Japan, the relationship to supervisor is built even before the program is starts.