I like to create unique baselines and choose a Dynamic Baseline that only includes the major revision as the starting point. For example, choose embeddedEsx 5.0.0 for ESXi 5, etc and leave the other products out of it. Any non-applicable patches won't be applied, but this keeps the baselines a bit easier to work with. You could also created a Fixed Baseline and include only the relevant/(post-build on your ISO) updates. Either way will work.
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