This can be used as an experimental worker version with a custom modification of r5type select-link.
Adresses #913.

Modification format:

{
  "name": "Select Link SE Hawthorne (14)",
  "r5type": "select-link",
  "lat": 45.512003,
  "lon": -122.642333,
  "radiusMeters": 50
}

This will find all stop-to-stop segments on all routes passing through the area defined by lat/lon/radiusMeters. When a regional analysis is run with freeform point sets and "record paths" enabled, each path is then checked to see if it contains one of these segments, and only the ones passing through the zone are kept.

The selection point in the example modification is near a transit stop, so it grabs one segment of a few patterns in one direction, and two segments (on either side of the stop) in the other direction. This is indicated in the worker logs and returned as scenario application info for display.

2024-01-03 19:12:18,321 [pool-7-thread-1] INFO  c.c.r.a.s.Scenario - Applying modifications to TransportNetwork.
2024-01-03 19:12:18,321 [pool-7-thread-1] INFO  c.c.r.a.s.Scenario - Applying modification of type SelectLink
2024-01-03 19:12:18,909 [pool-7-thread-1] INFO  c.c.r.a.s.SelectLink - Selected links for CSV path output:
2024-01-03 19:12:18,910 [pool-7-thread-1] INFO  c.c.r.a.s.SelectLink - Route 14 direction 1 after stop SE Hawthorne & 27th
2024-01-03 19:12:18,910 [pool-7-thread-1] INFO  c.c.r.a.s.SelectLink - Route 14 direction 1 after stop SE Hawthorne & 27th
2024-01-03 19:12:18,910 [pool-7-thread-1] INFO  c.c.r.a.s.SelectLink - Route 14 direction 0 after stop SE Hawthorne & 20th, SE Hawthorne & 23rd

Below is an example of the output CSV. I used a set of 10 randomly placed points as origins and destinations, so there are 100 total origin-destination pairs. The output CSV has one single line per unique O-D pair, and only these 15 O-D pairs have any itineraries passing through the selected area. All the separate paths for that O-D pair are condensed into one (this is done in a self-contained post-processing step, and could conceivably be disabled).

The routes column shows all bus routes used in any itinerary that passes through the selected area. The totalTime column is the average door-to-door time of all itineraries passing through the selected area. The nIterations column is the number of times (out of 120 total) that an itinerary passed through the selected area.

origin,destination,routes,boardStops,alightStops,rideTimes,accessTime,egressTime,transferTime,waitTimes,totalTime,nIterations
ab532a5e,71ec93a1,48|14|100,ALL,ALL,ALL,ALL,ALL,ALL,ALL,77.1,7
57268260,71ec93a1,55|54|14,ALL,ALL,ALL,ALL,ALL,ALL,ALL,62.8,35
57268260,1e77cf67,55|14|72,ALL,ALL,ALL,ALL,ALL,ALL,ALL,91.8,14
a8dcb0fb,71ec93a1,55|54|14,ALL,ALL,ALL,ALL,ALL,ALL,ALL,57.4,38
a8dcb0fb,1e77cf67,55|14|72,ALL,ALL,ALL,ALL,ALL,ALL,ALL,86.3,9
d8932a64,71ec93a1,14|70,ALL,ALL,ALL,ALL,ALL,ALL,ALL,46.2,54
82eaeda4,71ec93a1,14|100,ALL,ALL,ALL,ALL,ALL,ALL,ALL,74.6,12
71ec93a1,396764f7,16|14,ALL,ALL,ALL,ALL,ALL,ALL,ALL,84.3,18
71ec93a1,82eaeda4,57|52|14|100|58,ALL,ALL,ALL,ALL,ALL,ALL,ALL,76.6,105
71ec93a1,57268260,54|14,ALL,ALL,ALL,ALL,ALL,ALL,ALL,66.3,72
71ec93a1,d8bb0bd6,14,ALL,ALL,ALL,ALL,ALL,ALL,ALL,24.5,5
71ec93a1,d8932a64,17|14|70|8|6,ALL,ALL,ALL,ALL,ALL,ALL,ALL,50.8,35
71ec93a1,ab532a5e,90|48|14|100,ALL,ALL,ALL,ALL,ALL,ALL,ALL,79.2,29
71ec93a1,a8dcb0fb,54|14,ALL,ALL,ALL,ALL,ALL,ALL,ALL,60.5,72
d8bb0bd6,71ec93a1,14,ALL,ALL,ALL,ALL,ALL,ALL,ALL,27.0,35

A known issue is that this single iteration count may not allow deducing the proportion of trips on this OD passing through the selected link, because some of the iterations may have no paths (the destination may be unreachable on some of the iterations and not others). One solution would be to include a second line for each OD present, where the routes field is also ALL, as a denominator.

I have only tested on smaller data sets (Portland, Oregon) but it seems to work as expected.

I implemented this as a custom scenario modification type. It doesn't really modify the network so it's a bit odd to think of it as a modification, but it has the following good characteristics:
a) Can be used as a custom worker version on the standard production system (without re-deploying the whole system)
b) Retains and reuses geographic intersection calculations to make it faster (the link selection step is a bit slow, making it part of the scenario means it's reused)
c) Doesn't require rebuilding the transportation network files, can be used on existing networks and scenarios by just adding one modification
d) Doesn't change the CSV output format, just removes all rows that do not pass through the selected area