I have machine basted my last two quilts. I use a long arm, but the idea should work for any type of machine quilting.
I baste both sides and top and bottom of my quilting area (in my case, this is determined by my throat space). I baste the entire quilt before doing any quilting. Once the quilt is fully basted, I then start my quilting at the top and I remove any basting line that might be in the way BEFORE I quilt that particular row. With an "edge to edge" long arm pattern, that may or may not allow me to do two rows before I remove another horizontal basting stitch.
We also have a sit-down long arm. I haven't used it this way, but I would approach it in a similar fashion. You probably would know how you will approach the quilting design (block-by-block, row-by-row, center-out, etc)..If you machine baste your quilt to match how you will approach it, then you should be able to determine when it is safe to remove a "basting boundary". For example: if I were using a "center-out" approach, then I might baste the outer edge of the quilt, then baste concentric circles from the center.
Don't know if any of that makes sense, but my basting on MY long arm leaves 10" x width-of quilt sections of the quilt that have no adhesive to hold the layers together. I DO have the tension from the rollers, but I have not had any problems with pleats or wrinkles with this method.