I don't think there exists any scientific literature on the matter because there hasn't been a real need for it. The worries of concerned consumers don't enter into the equation until something affects the bottom line. Pipe tobacco manufacturers put chemicals onto the leaf to avoid spoilage in order to avoid losses. It seems highly unlikely to me that there is a group of scientists working hard to identify the molecular constituents of 'that weird stuff in my pipe tobacco' ... there is no incentive to do so and it would, frankly, be a waste of time.
From another perspective, I notice that raw leaf in a jar never "grows" anything, except perhaps mold, if and when it occurs. Crystals and other oddities don't grow in bags of Gambler. Occam's razor leads me to put forward the rather rational explanation that whatever you're seeing in your pipe tobacco is exactly what the pipe tobacco manufacturers are putting into it. Pipe tobacco recipes aren't regulated by the FDA but to the extent you can identify what has been used in the recipe, I think you'd go a long way toward identifying what you're seeing as it changes form due to alterations in humidity and acidity or whatever else. Are microorganisms at play? Maybe. But these things appear in stoved tobaccos and baked tins as well, and the humidity of most pipe tobaccos (which, again, have been treated with agents to suppress growth) really isn't in the "sweet spot" required to support fulminant growth of microorganisms. You could use cutting-edge technologies and what you'd very likely identify is (suspenseful pause....) the recrystallized fruit extracts the blender used? Salts from the tapwater they used to rehydrate the leaf?
I'd be hard pressed to believe you're going to discover the laboratory website of Dr. Smith, FDA tobacco scientist, whose area of expertise is the identification of weird stuff in your tobacco using expensive modern techniques like mass spectrometry and nuclear magnetic resonance. Microbiomes are all the rage in research at the moment---people studying the "ecology" of different microorganisms and their interactions---in extreme environments under the ocean in deep sea vents or in geysers and hot pools at Yosemite, or even in your gut. Try getting funding from the federal government to explore microbial diversity on flake tobacco every time you see something weird growing on it.
Unfortunately for the more curious of those among us, more has been done to document the things that bloom on our foods, like cheeses and fruits, because these are generally more relevant to our health and commerce. Although I'm also incredibly curious about what these things might be, I'm also fairly comfortable with being agnostic about details like this that don't have a massive cost-benefit-detriment impact on my daily life. For my part, if the tobacco tastes good, I smoke it. If the cheese in the fridge smells "off" I throw it out, and I don't give it much thought. But I like my tobacco and cheese and breads a little funky---homogeneity is boring. I feel like an uneven cut of tobacco with weird crusts and things growing on it is probably going to have more layers of depth and hold my interest longer than a homogenous boring monotone.
... with the exception of beard hairs and bailing twine. Unless it's obviously spoiled (and your natural instincts and innate senses will tell you it's spoiled) none of the gremlins growing on your tobacco are likely anything other than the ingredients of that tobacco reassembling themselves and they're completely harmless.