Will Going Under the Muscle with Interfere with my Workouts?

You have described the tradeoffs well for lean and athletic women. You need coverage but under the muscle poses problems with distortion of the breast with muscle activity and generally unfavorable appearance; overs look fake because there isn't enough "padding" of your own tissue. The subfascial option or the split muscle technique is often a very good choice for women in your situation.

Without the benefit of seeing your photos- you described yourself as thin and active. I'd say the safest place for your breast implants would be behind your pectoral muscles. For a variety of reasons, implants seem to perform better and last longer in the sub-pectoral position. In addition, your long-term 'look' after augmentation will likely be better.
There are varying opinions on this issue- which I'm sure you'll hear about. If you are fit and have tight pectoral muscles, it will take some time for the pectoral muscle to relax with the implant beneath them. Consequently, your implants will sit fairly 'high' on your chest wall for a few weeks. The pecs gradually relax and thin, and the implants settle into a better position.
I recommend to patients that do pectoral muscle exercises (bench press, push ups, flys) to curtail these movements from their exercise regimens. These movements tighten the pectoral muscles and can displace the implants out to the sides, which may be noticeable while you are performing the movement. You may also find that you are weaker when doing these types of exercises.
There is no reason why you should not be able to do other types of weight-lifting exercises with your arms, and do aerobic exercise, after your augmentation. I tell patients to wait 6 weeks after augmentation before starting to lift weights again. You can begin walking, treadmill and elliptical machines as soon as you are ready after your augmentation.