So I just came across this thread and I managed to get it to work (However this is only a MAC fix) on Sequoia by gathering the knowledge here.
I was having the same issue with the MX Master 3s.
I have used a mixture of tweaking Apples Mouse settings and Logi Options+ on Mac
Scrolling speed is on the 2nd last notch (speed needs to be fast.)
Logi Options I Set Scrolling Speed to 100% Turned On Smooth Scrolling Turned Off Smart Shift Set it to free spin (this is your choice.
I think the main culprit here is the Smart shift if you are using it. Smooth scrolling works better in this but perhaps try it without Smooth scrolling.
Hope this helps someone, and hope it works for you guys on the MX Master 3.
Cheers