I went from tall enclosures to short for my rats and never noticed a difference in quality and health, in fact, the increased floor space seemed to created a better atmosphere.
I have noticed, if you go from short enclosure to tall, your rat could have difficulties reaching the food. They will also have difficulty jumping after not being able to for so long. Long story short, I built a rack out of tanks last year. The rats never had a problem reaching the food or water valves. I built mortor tub racks and sold the tank rack to my brother. He stocked his tanks with adult rodents that were raised in the mortor tubs and they could not jump, at least not as far as the rats that were raised in those same tanks. He has to use feeder bowls until they rotate out.