All have been done from a true floppy disk and disk drive - No emulator involved here !
(Same Disk + drive for both format)
You can get the dumps (AFI format) and the pictures there :
https://hxc2001.com/disks_analysis/ST_TOS_FC3_FORMATS
TOS Disk layout :

(High res) :
https://hxc2001.com/disks_analysis/ST_TO ... TS/TOS.png
One TOS Track layout :

FC3 Disk layout :

(High res) :
https://hxc2001.com/disks_analysis/ST_TO ... TS/FC3.png
One FC3 Track layout :

The track-to-track skew is different and there are some interesting tricks on the FC3 tracks :

The FC3 format goes quite far from the ST standard to gain some read/write seconds in the FC3 tool

The USB HxC use the standard format with ST files and take the exact format used with HFE files.
That's why you got the ST timings with ST files and that you have the exact FC3 read speed with HFE files (if you have formatted them with FC3 of course!)
Btw i am almost sure that the FC3 format can disturb some Games/demos loaders !
Some "real-life" tests are probably more interesting : How many time to copy a bunch of small files and "big" files.
This test both random and sequential accesses and this is how these emulators are mostly used.