Hi, I do a lot of signs with an mdf core with a maple veneer, I have good results in the following order.
1. Route
2. Stain (if desired)
3. Clear coat.
4. Paint (usually spray)
5. Sand
6. Clear
I clear before painting as it seals the grain so the paint doesn’t seem to bleed and the paint sands off of the clear easier than the wood and I avoid burning through the veneer as easily.
If I want to do more than 1 color I just mask the areas I don’t want to paint…