Job arrays in most queues can be chunked across an array boundary (not all jobs must belong to the same array). However, if the queue is preemptable or preemptive, the jobs are chunked when they belong to the same array.
For example:
job1[1], job1[2], job2[1], job2[2] in a preemption queue with CHUNK_JOB_SIZE=3
Then
job1[1] and job1[2] are chunked.
job2[1] and job2[2] are chunked.