You are correct - the primary advantage of the 140mm macro lenses (both RB and RZ) is flat field performance.
However they are also both optimized for distances that involve macro and near macro magnification work, rather than for work at greater distances, so when it comes to other aberrations, there will be some advantages when shooting subjects that aren't flat.
I'm not sure you would be likely to see much of those advantages when shooting flowers. I do think, however, that the greater working distance that the 140mm offers (as compared to the 65mm) might be more important than the greater maximum magnification offered by the 65mm. Adding an extension tube might be a better way to get that greater magnification.
I use my RB 140mm lens both for close focus and normal distance work, and it performs well in both situations. I like the field of view it offers.
And from time to time I'll get really close to something with the 65mm lens.