I'd agree with that except that you shouldn't really expect the timing marks on the t-belt to be lined up, or even there at all anymore unless the belt is nearly new.

In theory those two pins should sort of bracket the bellhousing alignment pin on the right side of the bellhousing (opposite the starter). But the funny thing is you can't see them when installing the flywheel (they must be used in the manufacturing process?). And in any case it's just easier to put the missing holes in the starter hole. This isn't a highly precise sort of alignment, the flywheel only goes on in eight discrete positions.
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'63 PV544 rat rod, '93 Classic #1141 245 +t