Grounding wires must be continuous from the main panel to each of the places they are going (ground rod and water pipe, same as in my house). As I understand it (and I went through this recently with my electrician as part of a heavy-up) only certain very limited types of connections are allowed - basically a type where they can't really be "undone". In other words, no wire nuts, Polaris or similar connectors.
To the extent that if there are two ground rods then the wire is continuous from panel to first rod to second rod, or if (as my electrician did) the water pipe bound is in two locations (before and after the original main shutoff valve) it is continuous from panel to first connection to second connection.
Thinking about it very practically, anyone doing work on your electrical system or who accidentally does something - oops, I cut this copper wire, what is it? - should not be able to do anything "normal" that would disrupt the grounding system. Disconnecting a ground wire in the main panel or at the ground rod or water pipe would be clearly "abnormal" so you would deal with it appropriately. But a junction box in the crawl space? That is a different animal. If someday someone is doing work and finds this box, they may have no idea what the purpose is and might check for voltage (none when nothing is going on with the grounding system) and disconnect wires to get them out of the way. On the other hand, if you find a big thick bare copper wire snaking through the crawl space, you will hopefully search until you find one end (main panel) or the other (ground rod or water pipe) and realize what it is and not disturb it.
But getting back to the actual problem: not enough knockouts. That is a solvable problem. You can cut additional holes as needed in the panel enclosure. You can also probably double up - two cables through a single knockout, provided the cables are small enough and the knockout large enough.