My walking foot always moves the top feed dogs (attached to the walking foot) forward, even when using the reverse button, which makes reverse sewing have a quite different stitch length than forward mode. I think most (all?) walking feet are made this way. You can do a quick test to check if yours is this way.
I vote for design decision - leave what you've got and FMQ something that appeals to you in the remaining unquilted border areas. You can go with something similar or something quite different. Have you ever wanted to learn feathers? Paisleys? McTavishing? Since the goal is to get the quilt done, you can use the borders as a learning and practice experience. Yes, things that are new to you are not going to look "perfect" or even excellent, but learning work is still good enough when looked at a reasonable distance.
Alternatively, if having similar quilting in the borders is important to you and you want to continue with the walking foot approach, I suggest sewing each line in the same direction (rather than trying to turn the quilt or use reverse mode). It'll be a lot of securing of the ends of sewing lines, but you'll get there. Slow and steady. One thing that can help to get straighter lines is to mark your sewing lines using a removable marking tool and a ruler. (Crayola washable markers are popular with many folks. Make sure to test it with a scrap of your quilt fabric before using it on the quilt!)
I'm curious exactly *what* looks different between your long-arm and DSM stitching. The stitch length? The evenness of the stitches? The tension? (is the thread compressing the batting a lot more in one mode than the other?) If you can tell us what appears to be the difference(s), we can try to suggest ways to adjust you DSM sewing to better match the long-arm.