Sstrhsrtj

I delved deeper into the details of the microtype package to get the best results and perhaps not the safest results. Three things are still unclear after reading the manual, hence a post here.

First, Microtype's options are default applied to the following font sets:

DeclareMicrotypeSetDefault[protrusion]{alltext}

DeclareMicrotypeSetDefault[expansion]{basictext}

DeclareMicrotypeSetDefault[spacing]{basictext}

DeclareMicrotypeSetDefault[kerning]{alltext}

DeclareMicrotypeSetDefault[tracking] {smallcaps}

The rationale to choose smallcaps for tracking is explained, nothing unclear about that. But the rest, why not choose all or allmath?

For the record:
alltext contains the conventional encodings, except the math encodings.
basictext contains the conventional encodings with some restrictions on the font's series, shape, and size. And again, the math encodings lack.
allmath contains the conventional encodings and the math encodings.
all contains everything.

Second, my current document has many symbols with sub- and superscripts in math mode. These symbols also appear in the body of the text and the visual results are often not very appealing if microtype disregarded them while taking the rest into account. I would like microtype to take them into account. Or is there is a good reason to let microtype disregard them?

Third, the manual states option spacing may interfere with the ragged2e package but without stating in what manner. Is the interference that complicated? I use the ragged2e package (with option newcommands). Can you reveal a bit more where I should be vigilant for if I enable the spacing option?
Update: I found the answer to why they interferes here. I am still wondering whether Robert's suggestion is a robust solution, and if so, why not include it in the microtype manual? Robert suggests (for RaggedRight):

setlengthRaggedRightRightskip{1pt plus 2em minus 1pt} % default is: 0pt plus 2em