Alternatively (to avoid having to reformat the interface due to the extra box), there could be a single box:
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And right clicking on it would display, in the context menu, these options:
Absolute coordinate (master)
Pixel coordinate (derived)
Pixel coordinate (master)
One of which would be checked (active). The first would store and show the absolute value. The second would store the absolute value but show the pixel value (and would automatically update when the comp resolution was changed. The third would both display and store the pixel value (and would resist resolution changes). A preference could be added to determine the default "coordinate mode" of new tools (giving those three options plus "auto" to use a default defined by the tool itself).
Interesting idea! In this case you could choose which parameters should be set in pixels and in normalized units. For example, Center of a polygon mask can be normalized whilst the Soft Edge and Border Width could be defined in pixels.
Adobe Illustrator uses a similar approach: you can either set a global option which units to use or you can type a postfix after the number in the parameter box (px, mm, cm) and Illustrator converts it immediately for you.
But don't forget that regardless the global resolution setting in the comp, different branches in the flow can have different resolutions.
That's why it would be good if the tools converted the units according to the input resolution. Here the difference between the master pixel values and derived ones would matter.
I thought about the master mode, so once you switch, the values are being converted, but then stored as pixels. I think, if you decide to define the center offset or the line width in pixels, you really want them maintain the same effect in pixels even though the input resolution changes.
This can be an issue with instanced tools applied to branches with different resolutions, but it's solvable as a special case.