I have not found a specific answer. It seems like most people that do this grow a ton more out than I’m capable in a home environment. So, my approach has been to save a couple seeds from as many crosses and pods as possible and grow them out to evaluate for physical changes. I grow them in stressed out conditions; 4 inch pots just to force early fruiting for evaluation. With this isolated seed I’ll do a larger test out in the garden with promising prospects. What do others do? I usually do the small grout during the winter and plant the seeds in summer following. Don’t worry, I haven’t made any gigantic leaps forward in any of my projects.
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fgene-13-1030536.pdf (2.5 MB)
The paper cited with trees and other data
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Does this mean, in practice I dont need to make any special effort to keep my annuum sweet peppers isolated from baccatum hot peppers - there’s a low risk of growing (or worse, giving out seeds/plants for) surprise-hot peppers unless the sweet peppers are mixed in with hot annuums or maybe chinense peppers?
I have two gardens (which I can use for sweet/hot isolation) one of them has a very good microclimate for peppers but the other larger one…doesnt. The larger garden is particularly miserable for heat loving baccatum species …or fully ripening/achieving the best flavour in sweet peppers.
If I can grow baccatum peppers alongside the sweet peppers without high risk of natural crosses (they can be in front yard vs. backyard/driveway area even - but not down the street) then the only peppers I need to banish to the other garden are annuum hot peppers and chinense …
I would definitely make efforts to keep pungent and non pungent peppers isolated from each other. You can bag flowers/plants/rows and have the physically closer to each other or you can separate them by a long distance. A third, intermediate, option is to have the peppers separated by intense pollinator friendly plants. This way they are likely to be complete with foraging before making it to the next row of peppers.
As it would be , if you want to cross a sweet and hot pepper they won’t be in bloom at the same time, but as soon as you don’t want them to cross they will do it automatically. I have had this problem before and a spicy pepper is unwanted when you planted a sweet pepper.
I guess I should clarify I dont mean placing hot and sweet peppers right beside each other alternating in a row, but in different areas of the same property (ie hot peppers in the front yard, sweet peppers in the backyard and beside the house) vs. my other garden is down the street 2 blocks away. Likely about 5 m / 15 ft minimum distance?
Also I’m very specifically asking about the risk of making surprise spicy F2 bell peppers the following year if I plant Capsicum baccatum hot peppers in the same urban property as my Capsicum annuum peppers.
It’s a bit of a quandary for me as I prefer to grow my sweet peppers in my home plot as I get higher production and sweeter peppers this way. This means Ive been planting all hot peppers at the other garden since I started saving seeds a couple years ago. Unfortunately I have found baccatum and chinense peppers sulk and dont reliably fruit at all in the wetter, less sheltered (so much higher temperature variation), significantly shorter season microclimate down the hill, whereas they went bonkers when I had then by the house. So I’ve considered swapping back, but then I would get fewer, less-sweet sweet peppers (at least in the seed saving population)
I’m totally fine with banishing cayenne and jalapeno down to the other garden and just planting a few extra of them to make up for lower production. I can also net over a habanero plant or two tucked in a corner of the backyard . However as my home garden is nearly all facing the street I try to keep it looking nice/decorative and dont want to net most of it - so planting all peppers here and bagging them insnt super tenable. The decorative thing does mean lots of unrelated pollinator plants throughout, though 
Maybe but unless your pollinators aren’t going around mixing pollens like you would in Mentor Pollination, there’s a lesser chance it could cross. If you don’t want to risk crossing, but still want to grow hot & heatless peppers together, plant a very different species form it’s own non cross-compatible group like a C. pubecens.
Natural cross rate between C. annum x C. baccantum is slightly lower than C. annum x C. chinense/frutecens (Same species practically) but not zero.
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I think Murphy’s law applies here. If it’s possible, it will happen. In this case it’s not even extremely unlikely and only thing that matters is how many you grow. If you grow 50 plants for example, changes are quite low still in any given year, but over years it all adds up. This said, cross between baccatum and annuum should be extremely easy to pick out when it starts to flower. At least based on what I’ve seen, the flowers are a mix of the parent species. Especially visible compared to annuums, but should be possible to distinguish in baccatum also. You only need to go through them once they start flowering. You could then remove it or possibly cover if you want to grow out F2s for someone to try out.
I Think that it can be done since peppers are self fertile. You would just cover the flower with mesh and let it pollinate itself. Once it sets fruit you would mark the fruit and that’s would be your isolated seed saved. This seems to be the general technique for many of the pepper seed farmers. Most will grow like four peppers together under one mosquito net. That way they can grow hundreds of varieties in one yard in a little bit. I can look for videos where they show their set up, but it’s pretty simple