limoric --- I've done that too with peppers, and had up to four in one pot ... and they did well too!
The point I was trying to make, is that they will do much better, and you will have bigger plants with larger harvests ... if the roots are not in to much competition with each other.
Cross pollination is a whole different 'ball of wax' ... Most people do not realize how important it is to prevent cross pollination of plants within the same species of Tomatoes or Peppers.
There are five species of peppers (Capsicum):
1) C. pubescens -- purple flowers and seeds (Rarely grown in the US)
2) C. annuum --flowers are white or purple and have tan seeds (one of the two grown in US)
3) C. chinense-- flowers have a greenish tinge and the ripe fruits have a strong smokey-tropical fruit aroma (Rarely grown in the US)
4) C. frutescens-- flowers have a greenish tinge , but the fruit has a vegetable aroma (one of the two grown in US)
5) C. baccatum -- includes escabeche, kellu-uchu and puca-uchu. (Rarely grown in the US)
Pepper plants are notorious for cross pollinating, and though it is almost impossible to prevent ... the mixing of different DNA from unrelated species does not alway produce desireable results.
Specific hybrids of both peppers and tomatoes have been selectively hybridized under extemely controled environments for years ... to get plants that have larger and better tasting fruit or hotter (in the case of peppers), stronger plants, more disease resistance ... etc.
It would be fun for you to see what comes of it though ... but in my doing what you are attempting to do, I came up with unsatisfactory 'offspring' from those seeds the next year.