Downsides to paralleling two separate strings is you will need two BMSs.
And if the strings are sometimes not in parallel, then separate capacity monitoring is called for.
Charging can happen in parallel, but only when the strings are connected.
Can you help me understand when you'd want parallel versus separate for the two strings?
Once they drift apart significantly voltage-wise, you won't be able to just reconnect them in parallel.
bobkart