It shouldn't matter. Will be more up to the hardware having quirks than FreeNAS. As long as the FreeNAS sees the disks directly it doesn't even care what controller they are hooked into.
In general, it is fine. More specifically, it is fine except in the unusual case where it isn't. Some combinations of SATA drives, especially failing SATA drives, have been reported to cause SAS expanders to do strange things creating device timeouts. This was probably more of "a thing" with the old SAS2 / 3Gbps stuff. This is also NOT a FreeNAS thing at all, but rather an underlying hardware problem, which will also have problems for Windows or any other OS.
So the strictly literal answer to your question is "no, of course it doesn't" because FreeNAS doesn't care.
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