By definition, you have chronic kidney disease (CKD) because the dysplastic polycystic kidney has been present for at least three months. Hence, you do have reduced kidney function. The body building that you are doing will increase the serum creatinine but it should not change your glomerular filtration rate (GFR). The estimating equations that we use could be inaccurate with your large muscle mass and a 24 hour urine collection may be more accurate for measuring your GFR (measuring your creatinine clearance by 24 hour urine collection).
Finally, the muscle mass would not increase the amount of protein that you are spilling in your urine, hence, this is quite concerning for kidney damage that is occurring for some reason. I recommend that you consult with your primary care physician (PCP) and discuss whether you need to be seen by a nephrologist.