It can only take a few generations to significantly improve a strain through inbreeding. That very inbreeding is why all guppies don't look like wild ones. The fancy ones didn't just happen along. Their characteristics were carefully chosen from among wild stock, maybe a color or pattern or fin shape came closer to what was wanted in a particular fish. After the choice was made, the fry were checked to see who was moving in the right direction and it was bred back to either a sibling or a parent. Eventually the target color or fin shape or whatever was actually seen in a particular fish, not just a hint of what it might be in some future generation. Next came all of the inbreeding required to "fix" the gene in a strain. Eventually a fish that produced that feature reliably was found and then you could count on the fish breeding true. Finally that fish strain was reproduced by the tens of thousands to make the fish in your LFS.
When I first started in the hobby, black mollies and red swordtails both commonly gave birth to a large percentage of the "green" color morphs. The red in swordtails and the black in mollies had simply not been fixed yet. The green throwbacks reflected the fact that the fish were not yet breeding true. Today you can count on black fry from a black molly or red swordtails from a red swordtail drop. The colors have been fixed in their populations.
After these many dozens of generations of inbreeding to develop a particular look from good starting stock, I don't worry about the trivial amount of it that happens in my tank. I am not that careful to only buy a strain that is breeding true and keep it well separated from other guppies. Even if I did, the breeding in my tank would go much like the commercial production phase of that long development path.