You're absolutely correct when demanding a detailed analysis. Basically, it's necessary to decribe jitter as parameter that depends on measurement bandwidth respectively period. A phase noise spectrum (frequency domain) or jitter versus run length (time domain) are suitable to represent it completely.
Altera device manuals also mention the ability of a PLL, to reduce jitter, e.g. from Stratix IV PLL chapter:
--- Quote Start ---
A low-bandwidth PLL filters out reference clock jitter but increases lock time.
--- Quote End ---
Other documentation parts, e.g. in the PLL chaining chapter, give the impression, that feeding a clock to a PLL would only increase
the jitter until you finally cause unlock. But they don't provide a detailed analysis. In the switching specifications, only maximum
cycle-to-cycle jitter is given.
I'm doing a lot of PLL chaining in designs and didn't yet experience problems, also any source synchronous serial link typically
does a double chaining: Master PLL to TX PLL, TX PLL to RX PLL.
But whatever the PLL behaviour in this designs may be (it's rather reliable, I think), it seems clear that the timing analysis can't consider the actual dynamic, bandwidth dependend jitter. It can just add up uncertainties.
P.S.: I don't agree with pcie-rat's comment on Altera's layout recommendations and reference circuits. You can see, that Altera has been playing around with suggested PLL supplies during the last years. But it's really a complex matter. In my opinion you must acquire an own understanding of good design practice. Altera has given valuable help in this regard, and they, first of all, have improved the PLL hardware by supplementing analog regulators.
I have seen other manufacturer's reference circuits (e.g. in the RF field) with part numbers and good sounding suggestions: copy the reference circuit and everything is perfect. You may want to believe it, until you ever measured their development kits ...