If your external NVMe SSD is limited to standard SSD transfer rates due to connection type it is nowhere close to utilizing USB 3 bandwidth. So the faster ports offer no advantage.
Standard SSD transfer rate:
Read sequential data 550 MBps
Write sequential data 520 MBps
USB 2.0/Hi-Speed: 480 Mbps.
USB 3.0/SuperSpeed: 5 Gbps.
USB 3.1/SuperSpeed: 10 Gbps.
But a natively connected M2 NVMe should be much faster
NVMe PCIe 3.0 (aka Gen 3) up to 3,500MB per second,
NVMe PCIe 4.0 (aka Gen 4) up to 7,500MB per second.
Also, all kinds of other factors influence boot speed.
Standard disclaimer: I am not a hardware guy.
My laptop was manufactured in 2019 and the original internal NVMe drive was upgraded but there was no decrease in performance when this was done. But obviously “your mileage may vary” depending on both the computer and the quality and design of the drive.
It is similar to the results one gets when benchmarking SD cards and USB flash drives. None achieve write speeds that are anywhere close to the theoretical through-put of the USB 3 standard. It is only when you use an NVMe SSD in a USB3 enclosure or a USB3 flash drive that actually is NVMe based that you even get close in very short bursts. Even the Sandisk Extreme Pro SD card achieves write speeds up to approximately 140 MBps in an adapter or device that can handle this. The fastest flash drives that I am aware of are the SSK USB 3.2 drives, they achieve up to 520 MBps and are NVMe based.
https://www.amazon.com/SanDisk-512GB-Extreme-UHS-I-Memory/dp/B09X7DZM1V?th=1
I wanted to assure you that I appreciate any advice and observations that you make about computers or aircraft.
Today, I upgraded the DDR4 memory in my laptop to 32GB. HP and multiple sources said that the maximum allowed on my motherboard was 16GB. But I read in a forum that another HP Laptop similar to mine with a different motherboard but also built in 2019 was capable of using 32GBs despite what HP said. I decided to try the appropriate memory in mine and incredibly it worked.
MSFS 2020 which is not suppose to run well on integrated graphics is now quite a bit more stable, and running cooler. FPS are only up a hair, but I am still extremely happy. Of course, I have it on low quality settings and at only 1600x900 resolution, but for training purposes is not that bad. X-plane 11 is also running better. I am going to run some benchmarks to quantify the improvement, but it is definitely running better.
When my wife and I come into a little money, I will have a choice to make... purchase a better computer and peripherals or put the money into upgrading my avionics more than I had planned.