Harmonics I understand but I'm not sure how it applies to my problem.
As I said I am able to get FM broadcasts available in my area and I do get a signal at 88.1 from the transmitter in the house. The nearby commercial FM stations are clear no matter if my transmitter is broadcasting or not but when I raise the antenna above the roofline - all bets are off and not all are listenable.

I can get the transmitter's signal (and commercial FM broadcasts) as long as the antenna is on the ground but they are not noiseless. As soon as I raise it, say to the peak of the garage roof, most stations I'm interested in get very noisy to completely unlistenable depending on the antenna's orientation.

Testing, I positioned it lying on the roof and oriented in several different directions. Some positions were good for one favorite station but not the other and none of the positions I tried would receive both the two favorite stations and the transmitter.

When I bought it back down to ground level I could find a spot or two that allowed reception for all frequencies, but again not clearly.

Due, I guess, to the nature of frequency modulation, at some times of the day no amount of re-positioning the antenna would allow getting a clear signal from the more distant commercial stations, only the nearest.

Moving the equipment to another area of the garage made a huge difference so I'm thinking wiring in the garage might have affected the signal path.

Sorry I don't understand what you mean by "...have some separation between the two..." they are now 50' to 75' apart, wouldn't that be sufficient? - and what sort of filter are you referring to?