Scrolling with the Logitech MX Master in Safari sucks out of the box. The following from this Reddit thread helped, even though it required installing 2 additional packages.

Here’s the useful part of that thread:

Install Logitech Options+ (sigh) and set:

Logi Options+ (Plus): Customization App for Logitech Devices

What a gross bit of software, but it’s necessary here. I’ve read that once this process is done, I can delete the app completely, but I haven’t tried that yet.

• Scrolling speed: 0% (as the OP says, this is the most important option to set).
• Scroll direction: Standard (I would set it on Mos, but you have to pick one here anyway).
• Smooth scrolling: Off (also good to turn off, Mos will take care of it instead).
• SmartShift: On (If you want it).
• Sensitivity value: 95% (we’ll see, maybe I’ll take it down to 90%).

Install Mos:

Mos | Smooth your mouse

brew install mos

(Note that launching Mos required xattr -d com.apple.quarantine Mos.app)

• General > Smooth scrolling: On.
• Advanced > Step: 75.00 (at least in my resolution, anything lower than this is just not enough of a scroll per ratchet movement).
• Advanced > Speed: 3.50 (didn’t try too many others, but it seems to work in conjunction with the rest).
• Advanced > Duration: 3.90 (default value, haven’t played around with it yet).
• Now the ratchet action works as expected from a normal mouse, but when I give it a little nudge it goes into a free-spin and scrolls fast. I don’t know how much accuracy I’m getting with the free-spin yet, but to get to the bottom of a document, it’s great. I’ll update if I keep playing with these settings.

Once I’d done this, scrolling in the MX Master has been like butter.