Mixing x into permutation through XOR vs. modular addition
Either operation works as long as one operand (or both) is unpredictable and the two operands are (practically) statistically independent. Normally XOR is used because it requires fewer transistors and less time than modular addition in hardware based implementations. 

In software both operations run in one cycle for data that fits a register size. This gives addition an advantage over plain XOR operations. Differences in inputs to the steps of the permutation propagate faster with additions because carry bits influence the probability that an output bit may change.

ChaCha is primarily meant to be used in software implementations on machines with native support for 32-bit modular addition. Replacing the final additions with XORs is very unlikely to effect security, so the choice may be arbitrary.