Ruag... Sie sind aus Oberpfaffenhofen?
Thank you for the post, nice to see the link is working again. To answer your questions, the bearing load is determined by an FEM as you noted, then incorporated into the compounded stress intensity factor solution as described in Appendix B of the RAPID Analysis Methods Document or Appendix E of the RAPIDC Analysis Methods Document. Testing shows there is no hole-to-hole phenomenon like edge proximity effects for cracks growing towards a free edge, though one would imagine there should be something observable like that.
The FAA does not "endorse" any computer program, even with all the posturing the individuals are smart enough to avoid such appearances. A bit of history: RAPID was developed in anticipation of the Aging Aircraft Rule which required a large number of repairs to be analyzed for Damage Tolerance in a short period of time. So the model was like SFAR 36 operations - have a technician plug and chug, then have the DT expert review the results and make the recommendations. This is why the passwords and report title pages are set up the way they are. In the end, RAPID didn't provide much advantage over SRM repairs and besides the OEM's started generating usable data anyway. Then, the Small Airplane Directorate provided funding and the Tech Center managed the contract to develop RAPIDC for commuters. Things just ran their course, airlines disposed of their 402's and Merlin/Metros, so the funding stopped (around 2005). Of course you won't get feedback; Dr. Shiao left the FAA this past summer.
RAPIDC (and RAPID) are somewhat limited in the problems they can solve, namely repairs and connector hole doublers in cylindrical pressurized fuselages. Symmetry is another constraint. But the time savings are enormous, and the majority of day-to-day mods can be done. Can't do wings and tails, and flat bulkheads are nigh impossible. AFGROW and NASGRO can do all those and more; of course(!), you are on your own to develop loads, stresses, fastener pattern loads, and model SIF's. If anything, I'd be more worried about the variability and poor assumptions rather than a program (which does all the hard preliminary stuff) being "too canned." But in the end, the output of all these programs require interpretation and implementation (inspection program development).