Thanks for the reactions everyone. Tons of great questions, many of which I asked last night during the long conversation with my son about these issues. Here's some of the stuff we did talk about, because I had many of the same thoughts you guys have:
On bacteria: It may or may not also be present throughout the tobacco. The visible stuff was only yeast and sugar. He showed me both under the scope, but unfortunately I don't have a scope-mounted camera to take pictures for you guys.
Why don't tobacco manufacturers produce yeast/bloom on purpose? Great question. He pointed out that all the big beer brewers have biologists and genetics scientists on staff to ensure the purity and survival of their preferred yeast variants, as the beer industry deeply understands the impact of yeast on the taste of their final product. It seems like pipe tobacco blenders primarily stick to tradition and doing what works.
On Enzymes: I didn't ask. I can follow up with him on that topic.
On seeding tobacco with other yeast: Great question Woodsroad. I actually asked that in multiple variations. Including - "what if I took a flake of Stonehaven and put it in jars of other tobacco?" I also wondered if the yeast found in the Jersey Isles (Germain/Esoterica) could be distinct from the yeast found in Carolina (C&D). He conceded that might be possible, but without scientific testing didn't think that was a real strong hypothesis. He also thought the yeast colony would max out reasonably quick, so adding an aged piece of Stonehaven to a freshly opened tin might not do much. Apparently common yeast is exactly that - incredibly common.
On Oxygen: His warning was once the tin is opened, oxidation is going to start and it is a relatively fast process. Here's an analogy he used: You age a bottle of Bordeaux for 20 years because it improves slowly over a long time. Open it and drink right away and it's probably very good. Put it in a decanter to "breathe" (oxidize) for just an hour and it's sublime. Try to drink it a week later and it's ruined junk. Now apply that to tobacco only much more slowly.
Some of his advice to me (as a guy with 50+ pounds of tobacco aging) -
1) Buy smaller tins. Once you open the aged 8 ounce tin the tobacco will change before you can smoke it all.
2) Once you open any tin, if you intend to age the tobacco then get rid of the oxygen. He suggested either packing the mason jars full, leaving little space for oxygen, OR - leave space in the jar and light a tea candle (unscented of course) and seal the jar. Oxygen is roughly 20% of our air. The tea light goes out at about 5% oxygen concentration, which is after 75% of the oxygen has been removed.
My own additional thought: Think about how tobacco is packaged. Esoterica eight ounce bags are practically vacuum sealed with little to no air (oxygen) present. Their 2 ounce tins are packed full. Then think about tins with plenty of air space (McClelland, C&D, etc). It seems like that could be making a real difference, although my son thinks the oxygen gets depleted pretty quickly in any sealed tin.