Oh, this is my wheel house actually.
So, merle is a very unstable gene. Even in breeds where it occurs naturally (as in, has been part of the breed standard, and not brought in through outcrossing), it can change between generations because it's a form of mosaicism.
In the majority of cases, it only effects eumelanin (black pigment), so you will only see it on dogs that are able to produce black pigment (this includes dogs who are bb, which are liver/brown, that liver/brown is eumelanin).
SINE length is very important when it comes to merle and how it effects the pigment. I won't get too much into what SINE is since it's complex genetic stuff, but long and short of it is that the longer the SINE insertion, the more pigment is deleted. And it is possible to "mix and match" merle genes to lengthen the SINE to a point where the pigment deletion causes issues with hearing and eyesight.
There are a total of 7 merle alleles currently known, and 28 ways they can be combined. Some of them won't cause issues due to the stacking SINE length not being that long, while others will cause significant pigment deletion and thus, issues with the dog's eyes and ears.
Cryptic merle used to be seen as the merle that was "hidden" or in such small patches that it was easily missed. This is now called hidden merle. Hidden just means it's not visible expressed on a dog; it could be because the dog has no black pigment (recessive red) or has pigment deleted through the white spotting gene that hides the merle.
Actual cryptic merle is Mc or Mc+. This allele is technically merle, but it breeds like non-merle and does not express. A dog with two copies of these genes won't generally express merle either, it behaves like non-merle.
Atypical merle is Ma or Ma+. This one can cause some expression, but it doesn't look like traditional merle. It can sometimes be mistaken for a dilute dog, though sometimes patches of non-merle are visible. A dog can be Ma+/Ma+ and not have significant pigment deletion. Some dogs with Ma+/m don't even appear to be merle!
Classic merle or just M is what most people think of when they think of merle. M/M will cause a dog to be blind or deaf or both, and have significant pigment deletion.
M/Mc or M/Mc+ are generally considered safe, as is M/Ma and M/Ma+, though it can come out as an undesirable look, as patches of pigment are diluted differently and not as uniform as is preferred in a lot of breeds.
Harlequin merle is Mh and it's not the same as the harlequin modifier seen in Great Danes. This merle gene has the longest SINE insertion, and can cause a lot of pigment to be deleted all on its own. It does act similar to harlequin in GDs, as it often causes large patches of non-diluted pigment and often a lot of white on the body.
Due to the length of the SINE insertion in harlequin, it cannot be paired with any other merle allele. It's so long on its own that even Mc+/m is considered a medium risk (the only time it might be "safe" is Mc/m or Mc/Mc, since they breed as non-merle).
As an aside, phaeomelanin (red pigment) CAN be effected by merle in rare cases! This is usually in the case of dogs with a long SINE insertion due to multiple alleles interacting. In other cases, it is an illusion where the merle is acting on sable shading or agouti (sable isn't as common because it's not as obvious or flashy, and rarely occurs on agouti).
Now, why is it "safe" in some breeds and not in others?
In breeds where it is part of the breed standard, ethical breeders will colour test their dogs to ensure no accidental merle/merle breedings are taking place. This is even more important now that more of the merle alleles have been identified and can be tested for, since they can "stack" and cause issues even in a breeding that appears to be merle/non-merle. You can't show or title a double merle dog, so why breed for it?
Whereas in breeds where it is not the standard, it is bred in by BYBs because they fetch higher prices. They're often not doing the basic health tests, let alone colour testing their dogs before breeding. Breed a merle to a merle, and you might get a litter of all merles, which means more money! The double merle puppies are the ones who often end up in shelters because they're "undesirable" and disabled.
That is to say, double merles are still very much a thing in breeds where merle is "natural". There are BYBs in those breeds, there are oops litters, and back when testing wasn't as accurate, it was possible to breed a dog who didn't look merle to a dog who was visibly merle, and end up with a litter of puppies who were merle and double merle.
The issue with introducing merle to breeds where it isn't standard is because colour breeding is generally bad. If you're only focusing on the colour of the dog to sell pretty puppies, then what issues are you ignoring? And of course, cross breeding dogs and then saying the resulting puppies are NOT cross breeds isn't good either because a lot of naturally merle breeds are high energy working breeds. Lots of these merle dogs are going to pet homes assuming they're low energy companion dogs, and then it turns out that it isn't the case.
It just comes down to poor breeding practices, and the lack of care a lot of BYBs have for the puppies they produce. Seeing a merle dog from a breed that just doesn't come in merle per the breed standard is just a big neon sign that says it was produced by a BYB.
