Here is a good picture of the level of black beard algae I’m attacking. Ironically it's cleared up from a large portion of the tank (while also turning my plants pretty bare in terms of leaves and whatnot). Otherwise, dosing hydrogen peroxide seems to be attacking it head-on without any major issues that others have faced. I've moved the water outlet pipe (the dry dock is wet in the photos since I was testing where to move it towards for better water circulation), and have slightly shifted the dry rock back a little bit to anchor it down better as the turtle is digging randomly which has shifted it forward and made it wobbly.
I do have a few baby cichlids roaming the tank (which can be seen by other screenshots I took today), and the turtle is healthier than ever. Still has the odd spot on its shell that did appear as shell rot when I first picked it up, but at this point, I believe it's just the coloration since it hasn't gotten worse or better over the past 2 years.