Will i mess up the pot if roots get damaged? or can i lose some roots, transplant the plant and then will everything be okay?
So long as you're careful, and don't entirely rip up the roots, the plants will recover if repotted. So long as the root systems are developed, you literally could just depot all the plants together, chop through the soil, then repot each of the three. You don't want to rip apart seedlings this way. . .their root systems aren't robust enough yet to handle it.
You're just going to set them back a few weeks in growth while they rebuild their respective root systems.
If you don't mind waiting, and have the ability to grow out multiple plants to maturity at once, this is a perfectly viable option.
The biggest problem with multiple plants next to one another is **NOT** that the
roots will compete for space. . .its that the PLANTS will compete for LIGHT. With each plant shading its neighbor, they all try to stretch to the light to beat the ones next to them, and you end up with tall long stretchy stemmy plants.
So if you decide to keep the plants in the same pot, what you MUST do is TRAIN them (ie bend and/or prune them) so that the bulk of each plant is away from its neighbors. I'd bend each of the three away from the center so the stems are horizontal and in a "Y" shape. Then later, you can cull any males, should they appear.