If you're going to fully flood the 3 gallon pots and only have minimal medium inside, you should be fine.
Can you post a picture of your system?

Peppers will do ok in that size pot. This one has lived in a 20L planter filled with hydroton for the last 5 years. The blue pipe is part of the manual flood and drain system.

Great to see you got 5 years , I have just planted one in my DWC

Overwintering gives you a huge headstart on the season. I cut the plant right back so it lresembles a stick and flood it once a week over the winter. Never tried overwintering with dwc but its worth a go. When the plant explodes into growth in the spring you take cuttings to provide enough plants for the season.

Hex in my climate I grow outside all year long as the temperatures hardly go below 10C. so I think I should be able to grow all year long in my DWC as I do in my soil garden.As for cuttings that is a good idea, I must try.

I will be doing a ebb and flow garden indoors in the next month. I will be growing with rockwool cubes then transferring them to 6x6" square pots. I will be posting progress as I grow.

The square pots are interesting because they save a lot of space. I will most likely be using determinants as well.or I will single stem an indeterminate and wrap it around the table.