I would figure the same thing too. I've never actually changed just the boots on past repairs that I've done (always just replaced the whole axle) It would probably feel a lot looser when replacing just the boot since everything is already worn in while a brand new / remanufactured axle would feel a lot stiffer.

I had replaced two front axles a few years ago on an AWD car and the axles were really stiff (they were remanufactured) I was a little worried since I felt they were really stiff and may cause some issues but after installing them and driving around, they worked fine. I did keep an eye on them for a while but no issues ever until I sold the car many miles later.