That size container should be more than enough! I have somewhat large rose-scented one that I just chopped back for cuttings last weekend and it is in an 8" pot that is probably about that deep. I recently repotted a rose-nutmeg one from the little 3" pot that it was in to a decorative 6". As you probably know, these can get real leggy (I had some stems that were going on 3ft long on the variegated rose-scented...lol), so doing what you suggest shouldn't be a problem. Just make sure that you have a good soil mix in there that will dry fairly quickly since the scented (and regular) pelargoniums like drier conditions. If you are worried about them intermixing roots, you could actually pot them in their "overwintering" pot and sink that in the windowbox (where the windowbox has soil in it), and cover all the sunk pots with some decorative mulch or equivalent to hide their rims. Make sure that the pots have drainage too. That way the plants can grow lushly but will still be separated. If they get potbound, the roots can grow into the surrounding soil of the big windowbox via the drain holes, AND you can more easily pull them up in fall to bring inside. That should be neat to do.

I too am EXTREMELY SENSITIVE to poison ivy and recently broke out in a similar rash after being careless while propagating my all time favorite plant, the philodendron micans. I also suspected that had to be it so I took a fresh cutting and dabbed the sap several times in my arm and didn't wash off for a few hours. Somewhere between 12 & 24 hours later, I started feeling that familiar itch and watched as my test patch gradually spread out the size of a dime and rose up with the little tiny bubble pattern I'm used to seeing with poison ivy rash. THIS SUCKS! I'm in the middle of battling it right now and in my research found this helpful article. I also read another helpful tip that said the sap from these plants can somehow penetrate through standard medical gloves so thicker gardening type gloves should be used when propagating and caution should also be taken when refreshing propagation water. I plant to purchase some thick, SOLID rubber gloves that can easily be thoroughly washed. NOT those gardening gloves that have a breathable section at the back of the hand and wrists! You should also clean the tools you use and the work area. Rubbing alcohol AT LEAST 70% grade is known to be effective for cleaning tools that have come in contact with poison ivy so I plan on implementing that. As well as never shortcutting again by taking rushed cuttings and not doing the basics like laying out a protective mat and immediately washing my hands afterwards. I lazily let my NUMEROUS cuttings drop to the floor (CARPET!) and I know I didn't wash my hands right away like I normally do. A couple hours later I laid on this floor in a tank top and got a mild rash a day later across my upper back and shoulder area as well as my ear lobes which I believe is from handling my earbuds right after propagating my favorite plant. PLEASE MAKE MY PAIN WORTH IT AND LET THIS BE A LESSON TO YOU... PUH-LEAZE!

Leave them for now, they are too young to pinch. The habit of ivy geranium is more vine like, it's not unusual to find some of the stems longer. If you want bushier plants later, pinch back the growing tips when your seedlings have gained a bit more size and have more than one leaf per each stem. Pinch, or cut, just above a leaf - clearly you don't want to do this when a stem has only one leaf. :) There is a latent growth bud located at the node (node = the point on the stem where each leaf is attached). Cutting of pinching off the growth just above that node will cause that stem to branch out. More branching will mean more flowers. Some longer stems on ivy geranium aren't necessarily a bad thing though...leaving some of the longer growth to spill over the side of a large container or drop down from a hanging basket may be desireable too, depends on how you plan to use them.

I'm no expert on geraniums (or anything else for that matter!) Could it be the light these plants are receiving? I have a duckfoot ivy (different plant being used for comparison). Description on Internet says leaves stay well below one inch in size. I notice in too much sun the new leaves grow smaller & smaller (1/4 inch!) and are packed so close together that it doesn't appear as an ivy form anymore, more like a little bush. Pull away from window (like 15 feet away, bright but no sun) and leaves become larger in size (over that one inch size) and nodes lengthen and the ivy looks good again, given time. Other idea - could this be how a sport develops? Especially considering the fact that it trails! That growth hormone is very commonly used by greenhouses - they can grow a plant to bloom size but with less mass, so can stuff more plants on a shelf. I don't know how long that hormone stays in the plant to keep it compact, you would think it would be meant to be short term so that by the end of summer you'd have seen more normal sized leaves. Isn't BIGGER better!?