Why does Simpson Strong Tie require nails that would protrude beyond the rafter they're penetrating?
They don't.
The table lists rated uplift loads for particular installation scenarios, presumably with the largest nails that offer practical benefit. It doesn't list installation requirements. See footnote #13 for some clarification. It describes loading for alternative fasteners:

Allowable DF/SP/SPF uplift load for the H .2.5A fastened to a 2x4 truss bottom chord and double top plates using (5) 0.131&quot; x 1-1/2&quot; nails in the top plates and (3) 0.131&quot; x 1-1/2&quot; nails in the lowest three flange holes into the truss bottom chord is 260 lb. (160).

There's also a column toward the right side of the table that mentions 1½&quot; nails. You can see that uplift load is substantially less (540) for short nails than it is for long nails (700).
2½&quot; nails are mentioned for those (rare) cases where you have more depth to nail into. In those cases uplift data is important, so it's listed. It may also reflect the highest load rating achievable with that particular part.
You should use 1½&quot; (&quot;teco&quot;) nails into the truss chords (or rafters) and longer nails into the wall plates. This is standard practice. I've done so many times myself under inspection situations.