I think if they were legitimately substituting another substandard product and you could prove it you would have one hell of a lawsuit on your hands. I also think most cigar manufacturers aggressively protect their brands and would be unlikely to undercut the quality of their own product this way. Cigars more so than many products rely heavily on customer loyalty and repeat business and this is independent of where they buy their cigars. Do you think they would really risk alienating there regular customers this way? I don't think so.
I suspect this perceived difference is just that varied perception on the part of consumers. It has never occurred to me to take my from the internet cigars into the B&M and compare side by side but I have bought enough cigars in both places that if there was a significant difference I think I would notice. Regardless most manufacturers match color by the box even in the same blend so that if you did take to legit cigars from two boxes they may not match color identically. Cigars are a natural product with natural variation from leaf to leaf. As was already mentioned much of the difference is likely to be from variations in storage condition if not just the natural variation in the cigars themselves.
In the example of gurkha and many other retailers there is not that much A+++++ quality leaf around period and most of their lines have none of it but that is not some conspiracy to give one retailer better quality than another it's that they just send out a bunch of PR BS about how special the wrapper is for every freaking cigar. For the most part you pay more either for better tobacco and blenders and some you pay for marketing and packaging and for some you pay for all of the above plus a premium for scarcity same as any other industry.
I don't think they are creating two separate lines one for online retailers and one for everyone else. The most I could see is sending one batch to a set of lesser skilled rollers to crank out for the online retailers and the rest going to more experienced rollers. That still might not be a conspiracy that could very well just be a manufacturing reality. Have one really big order it goes to the largest pool of workers (lowest skilled) and the others go to higher skill workers. Still I even doubt that is the case.
As for the whole 75% off thing that is also marketing. MSRP for all but the most scarce cigars is a joke. The real difference is in not paying for retail space, knowledgeable employees, buying in bulk and not having to pass on state taxes take all that into account from the real retail price which is already well below MSRP and there is your 75% off. You see a stick in a B&M at MSRP they are making a profit after having had to pay all of those other costs that internet retailers don't. Internet retailers can take even a smaller profit margin if necessary because of volume. Just my