Physical fitness and internal fitness are connected, but they are not the same.
Yes, it's possible to be physically fit but not internally fit. Even many elite athletes have compromised gut health. The health of your gut microbiome is affected by whether or not you exercise, and it also involves what you eat, how well you sleep, how much stress you have in your life, and what types of exercise you do (for example, endurance sports can sometimes negatively affect your gut health). Fortunately, there's a test you can take to find out your Internal Fitness™ scores and what you need to do to improve them. Check out what's included in the Ixcela plans.