1) Yes, you can create new account key, configure with different G/L account and assign it to your pricing procedure.
2) No, the FIFO/LIFO calculation won't be affected. The tables MYMP (Period stocks) & MYMP1 (receipt data) will be get updated with both material value and freight value as per standard.
3) No need to include any new account key in the source code, the system will extract all GR cost including freight cost during FIFO/LIFO valuation however the account key usage is a customized one.
The above mentioned explanation is my understanding based on the test cases I worked. Please first evaluate in a test environment (DEV) before making any changes.