Darrell, the color won't make a bit of difference, and congratulations on a nice model of tractor. Yanmar didn't paint it; probably the dealer did. There are a few dealers who re-paint the Yanmars in JD colors. Best we have been able to figure is that they do this because they figure that the JD/Yanmar connection makes this a reasonable thing to do. Maybe it is a saleability thing. I have noticed that these dealers often try to play up the JD/Yanmar connection in a direction that emphasizes the JD side. My personal opinion is that these dealers are missing the point, but the color won't hurt your machine. Yanmar did make complete tractors for JD in the 80s and early 1990s, though recently they are only providing subassemblies to the JD compact line.
My YM336D has yellow turf wheels on it from a JD1050.....My wife thinks it looks silly....Yanmar red with yellow wheels. Nobody is going to loose it in the field, that's for sure.