Both Dim Pro and Rapture come with many options for their microtonal capabilities.
The the mulititude of .scl files that it uses to map to that many different scales are created with this tool.
http://www.huygens-fokker.org/scala/ You'll also find that harmonic relationships can even be seen with a tool called a harmonograph which not suprisingly show the prettiest patterns when some tonal combination is likely to sound pleasing also.
For some using standard tuning systems but slightly flat or sharp from A=440 are said to be of some benefit but that is likely going to be to do with specific listeners rather than having a universal benefit.
You'll find out that what you are trying to do is a very involved subject that many mathematicians, philosiphers, musicians and all kind of sound adventurers have been fascinated and engaged in for aoens.
Fortunately you don't need a rake of complicated and expensive equipment to get involved yourself, but it's not a subject for the faint of heart or if you are expecting to stumble on some incredible breakthrough in half an hour. Like I say many great minds from Pythagoras onwards have got immersed in it before now and there's not been a better time for anyone to join in.
Good Luck!