Yes, as long as FLSA and Pay Cycle (e.g., MO or BW) are aligned across all active jobs, the compensation can differ among those active jobs (e.g., one job pays hourly while another pays a set salary).
For example, UCB wishes to pay an exempt reader as biweekly hourly (1BH), and the second position is a graduate student instructor that pays a set monthly salary. As long as the appointments have FLSA and Pay Cycle alignment, this is acceptable