you can cut your fabric any way you want to.it is yours, you paid for it, and no one is going to show up at your door to say you can't quilt anymore because you cut that piece wrong!
some people do not like to seam their borders and buy 3 yards just so they can cut it lengthwise...it is their choice, nothing wrong with it...if you have a 3 yd piece of fabric and you are cutting 4 (6" borders) from it-- that uses 26" of the width of the fabric (adding the 1/2" seam allowances) which is going to leave you a piece of fabric 108" long (3 yds) x 18" (what's left of the width of a 44" piece) if you can work with that...i see no problem.
i do both, sometimes (usually if i have a long enough piece) when ready for borders i cut them long...if i'm going to still need larger pieces of that fabric i cut across the width or if i don't have a long enough piece to start with i cut across the width...it just depends on the moment...never since 1976 had someone tell me i can't cut my fabric up any way i want to....other than advice to watch those pesky stretchy bias'