Check your BIOS settings and make sure your GPU's x16 slot is set to the correct PCI speed. Some BIOS can do multiple PCIe speeds, and can be changed between 3.0 / 4.0 / 5.0. Many ship with this set to the lowest default. Also, the auto setting may not properly detect.
Also, while most say x8 doesn't make much difference from x16, it still can be a consideration. Some boards will cut the primary x16 slot to x8 if another x16 / x8 slot is occupied. Also, if you have two x16 slots, the GPU should be in the one closest to the CPU.
While I know AM5 is not AM4, something I discovered myself in my 5900X build -- AM4 Ryzen and supporting boards are REALLY fussy about RAM, and if it's not on the board's QVL list for that processor, it's either untested (questionable) or likely to be unstable, and could still be a consideration, as it could just simply be an AMD thing.
When it comes to RAM, it doesn't take much to create stability problems that can affect performance, especially at overclock speeds like 6000. Timings can be an issue as well if they're not correct. I understand that EXPO has been a bit of an issue for some users as well -- No offense to those with AM5s, but this is one of several issues I've seen and read a lot about that make me really glad I built a 5900X instead of an AM5. I've seen and read similar regarding the 4090, that perhaps it's not all it's cracked up to be, or at least not that much of a performance increase over the previous generation.
But perhaps this just comes down to poor tuning and bare minimum defaults. What are your thermals like (CPU and GPU)? Good thermals are a bit tricky with AM5 due to common air gaps between the IHS and cooler base plate, and thermals can be a huge factor in performance as excessive thermals can cause CPU throttling that can affect GPU performance. If thermals are an issue, you might try undervolting or tweaking fan curves to keep it from throttling.
Also, using Ryzen Master has my 5900X boosting to 5.0-5.025 at times. Runs 4.8-4.975 pretty consistently. While I'm not sure if Ryzen Master works on AM5 (or if there's perhaps an AM5-specific version), you might check as to whether the CPU is running at peak performance, because that can affect GPU performance too.
As for the overlay, I have noticed occasional inaccuracies in Afterburner as well, especially when compared to Nvidia's overlay. Something a lot of people aren't aware of is that GPUs can sometimes drop clock speed under reduced load to save power, which can impact performance if the firmware guesses wrong.
FPS is not a huge issue for me as my 60 hz 75-inch TV limits me to 58-60 fps, but I noticed some stutters and 30 fps sags at times. I eventually discovered my Asus KO RTX3060ti-8GB-OC was dropping to 900 Mhz clock speed while gaming, which was causing the hiccups. I found a solution in EVGA's Precision X1 software.
Precision X1 allows you to store multiple profiles for optimum GPU performance. And yes, it can control power and clock speed independently of Afterburner or GeForce Experience (independent clock speed / voltage control must be enabled) and even has boost lock to 'force' a higher base clock speed if desired.
Asus lists my GPU's boost speed at 1785. I set a 1655 base clock speed in Precision X1, and it's boosted to as much as 1835-1905 under load (PCIe4.0 x16 with the Performance/Quiet switch set to Performance), with decent thermals, staying around 65C-68C under full load. Absolutely stellar performance. Haven't had a problem since.