In real life, the average horse is about 5 feet tall. The average door (where I live) on a residential building ranges from about 6'8" to 7'2". The average door on a commercial building tends to range from 7 feet to 8 feet tall. So I personally don't really think it's that weird for a door to tower above a horse.
And despite the fears of what I would see, I Googled "outhouse" just now and then clicked on "Images", and honestly, most of the results seem to show the top of the door pretty much reaching the roof. While I can't 100% envision what your attempted outhouse looked like, I don't suspect that it really looked all that abnormal.
While the FSM doors probably are a tad tall, I still think that they're significantly less abnormal than the RTP doors are. I personally think it looks less weird to have a door that's just a hair too tall, compared to a door that's way too short. I went and looked through a lot of my paid DLCs just now, and literally every single one had tall doors (a couple offered the choice between short and tall doors, but most just straight up had only tall doors). Just recalling them off the top of my head (so I may be excluding some), this includes Time Fantasy, Celianna's stuff, Kokoro Reflection's stuff, Winlu's stuff, Lunarea's stuff, VisuStella's stuff, Pop! Horror, Omega Modern, Shopping Spree, MV-MZ Trinity (which surprises me since it's so closely linked with the RTP), Essentials, and Essentials Set Z. So while I hate speaking for people other than myself, I think it might be safe to conclude that a lot of people prefer taller doors than what the RTP provides.
But at the end of the day, the only opinion that's really important is yours. It's your game, so what's most important is that you are pleased with the way in which your vision is being realized. If you feel that you would be unhappy with your game if you were to use the FSM sets without resizing the sprites or the doors/windows, then by all means, do what you gotta do. I'm just saying that if you were to use the FSM sets without going through that extra work, and I were playing your game, I wouldn't have any problems with it.
Unfortunately, I don't have currently have any fantasy projects of which to speak, so I am not currently using the FSM set. But I do own all the FSM packs, and I plan to start such a project in the near future.