I don't have any subchannel-equipped discs to try out, but there's an option in the P.E.Op.S. CD plugin to read subchannel data from inserted discs. It might do it at the same time it makes the ISO, or give you the option to do so in the ISO Producer GUI. If not, you can go into P.E.Op.S. and tell it to create a subchannel file from your disc.
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