Technically yes, internal clearance will also apply.
For mains isolation, this should be strictly followed, it is a serious matter and no shortcuts should be taken.
For patient isolation, the 1 MOPP isolation barrier (Type BF or CF) is often technicality and many test labs just go on component ratings (isolation voltage) and don't go so far as to pull apart dc/dc converters and check internal construction. For example, I have seen many products "passed" with transformers that only have enammel isolation for the internal transformer. In most cases it's not a safety issue, just a technicality. It could be a business liability though if a later engineer checks and calls out the non-compliance.
If the applied part is defib proof, or has significant working voltages (e.g. stimulator with 200V output) it makes sense to look for appropriate internal clearance, although note that often the values in 601-1 are overkill for secondary circuits.