if you use a 3-piece airlock, the suctioning problems with better bottles can be avoided easily by simply removing the inner cap momentarily. usually you're moving them for some reason or purpose like racking so breaking the airlock seal is no big deal. it is also minimized if you lift them from the bottom rather than the neck. they do flex though - for me, a small tradeoff for durability, affordability and light weight.
ive never been particularly "careful" with the better bottles and they look as good now as they did brand new. no scratching, i dont think ive ever seen one scratched on the inside. i think youd have to work pretty hard to do that.
i am much more careful with the heavy, slippery, fragile glass carboys i have - i use them as minimally as possible, primarily for vacuum degassing.