Modifiers are not used for “tools” like for R rectangle or P pen, except for ⇧ which can provide a related tool, like ⇧P pencil.
Related functions usually include the same modifier keys. For example, create component is ⇧⌘K and break component is ⇧⌘B.
It seems like some shortcuts were taken directly from Adobe products - a smart move. E.g. ⌘Y for outlines.
Important OS/Browser shortcuts seem to be avoided: ⌘W, ⌘Q, ⌘L (focus address field), ⌘N
Sometimes extra modifiers are added or used to avoid collisions. ⇧⌘L locks a layer without colliding with ⌘L. And ⇧H flips horizontally while avoiding ⌘H for hide. The inverse ⇧V flip vertically is grouped for semantic ease, also avoids ⌘V paste.
Figma provides a large number of shortcuts for fine control - things like font line height or object alignment.
Thoughtful controls for navigating the UI
Efficient use of keys - ⌥ 0 1 2 (nav) is totally different than ⇧ 0 1 2 (zoom)or 0 1 2 (opacity). And ⌘ 0 1 2 on the browser app is reserved for tab navigation, but the desktop app also has tabs, so it actually maps well.
I think they are following Apple’s guidelines sorta: Prefer ⌘ Command, then ⇧ Shift, then ⌥ Option though sparingly. Let’s take the case of number keys. First order actions get ⌘ - so ⌘0 1 2 control tabs, which matters most in a browser. Second order get ⇧ - ⇧0 1 2 control zoom, which is maybe most important to an editor. And third is ⌥ which controls navigation in the UI.
Organization
Essential
Tools
View
Zoom
Text
Shape
Selection
Cursor
Edit
Transform
Arrange
Components
Essential
0
Action
Shortcut
Description
Action
Shortcut
Description
1
Show/Hide UI
⌘\
Press it now to quickly hide the panes and focus on your work
2
Pick color
^C
Grab a color from elsewhere without losing your flow