Why does one blocked outlet put water inside the house?
Because a parapeted roof has nowhere else to send it. There is no eaves to overflow and no overhang to spill past, so water rises against the parapet upstands and the party-wall terminations until it finds the weakest joint. A gutter at the eaves spills outward; this one spills inward.
Depth builds faster than people expect on a small roof, and standing water loads every seam it covers continuously rather than for the length of a shower. A roof that would have shed a storm without noticing can leak in three places because one strainer was packed with granules.
This is also why clearing the outlet is sometimes the whole repair. On a night call in heavy rain, a blocked drain is as likely a cause as a hole, which is why a roofer attending an emergency checks the outlet before reaching for a patch.
How can a drain leak while still draining perfectly?
Through the joint rather than the pipe. The flange or clamping ring where the membrane is dressed into the bowl is a mechanical seal that can loosen, corrode or lose its grip on an aged sheet. Water then travels between membrane and deck while the drain itself keeps running happily.
Those leaks are deceptive because the obvious test, pouring water down the drain, passes. What finds them is ponding the area deliberately and watching the ceiling below, or looking at the deck from inside where that is possible.
The same applies to a through-wall scupper, where the sleeve can be sound while the membrane dressed into it has shrunk back a fraction. On an older roof with several generations of patching around the outlet, that whole detail is often best rebuilt rather than resealed again.
How often should outlets be cleared here?
After leaf fall at minimum, and after any heavy rain or high wind if you have trees nearby. Outlets fill with leaf litter, seed, roof granules and windblown grit rather than dramatically, so the capacity drops over seasons until a single storm finds the margin gone.
There is a winter dimension too. Philadelphia gets some snow most winters in totals that vary widely, and an outlet that is already restricted is the one that freezes and then overflows on the thaw. No snowfall figure appears here because the sources found for it conflicted.
Put it on a schedule rather than a reaction. Clearing a drain is the cheapest roof maintenance there is, and it protects the parapet flashing and the membrane seams that a pond would otherwise sit on.