Tuning
I daresay either I grossly oversimplified the tuning process or my organist friend did in his advice. What you describe is, of course, the problem of natural tuning, which was solved by tempered tuning, which became the standard method thanks largely to its championship by J.S. Bach nearly 300 years ago. Doing your own tuning takes a good ear at least and a good sense of relative pitch. Perfect pitch sense would be very useful, but few people have it.