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I wouldn’t be as worried about hybrid capture. The major frequency skew with PrimalSeq is because of preferential amplification of the amplicon with no primer mismatch vs the one with a mismatch. Since hybrid capture doesn’t have amplification, you shouldn’t have that issue.
You’d of course need to worry about difference in capture efficiency with probe mismatches, but I’d say that’s less of a concern. Also, hybrid capture typically have many more probes covering the target vs. PrimalSeq.
You have other issues to worry about w. capture though 
What are those other issues?
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. Also not so great with getting enough of the genome for intrahost analysis from relatively low titered samples - often incomplete coverage, in my experience.
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