its not the roots being close is the problem. its the nitrogen the corn will need and steal from the squash.

If you want to try the 3 Sisters method plant some peas or beans in there too, they'll add nitrogen, but 3 plants in a pot might get crowded.

I don't do container gardening but last year I would plant a double row of peas about 4-5" apart, then plant the corn between the rows a couple weeks later. It seemed to work out pretty well. The peas I planted were the bush variety, the kind that need poles might strangle the corn. I had squash too but bugs killed them :(