Racing in your aero position has more to do with saving energy than spreading the strain of a triathlon over different muscle groups, and there's no doubt that a good aero position can save you a ton of energy. Getting off the bike with more fuel left in your tank, so to speak, is absolutely essential to having a great run. However, this will only be the case if you've spent enough time perfecting and training in your aero position.
I (along with several of my top triathlon coaches) disagree with the notion that the ratio of road-to-aero training should be 90/10. If you're primarily a triathleteand that's the
Beyond developing discipline-specific power, more training time in your aero position allows you to adapt to the flexibility and handling challenges presented by the riding position. A lot of athletes get injured because they're not physically prepared for the demands of riding in an aero position for an hour or more at race speed. Training in your aero position will not only help you adapt to the bike, but may also help you gradually move to a more aggressive aero position in the future.
As for the stress on your knees and back, that's a function of the quality of your bike fit. When your saddle, bars, and cleats are all in the optimal positions, there's no reason you shouldn't be able to complete the majority of your training hours in an aero position. Keep in mind, that when I say "optimal positions," I'm not merely talking about optimizing aerodynamics. You have to take flexibility, comfort, and control into consideration as well. I encourage you to seek the expertise of a performance center (like our CTS facilities in Colorado Springs, CO, or Asheville, NC).
The 90/10 ratio is more appropriate for road racing cyclists who occasionally have to compete in a time trial. They need some time training in their aero positions so they can control the bike and compete without injuring themselves, but since the vast majority of their competitions are ridden on road bikes, spending too much time on the time trial bike can be detrimental to their overall racing performance.