slightly different, but both reasonable duplicates
This shouldn't really happen. Either the questions are close enough to each other to be duplicates of each other (and one of them should be closed then) or they are different and so the new question is a duplicate of only one.
Of course, reality is dirtier than that, and the case you described does happen. But computer systems which are programmed to be as complex as reality is use their usability quickly.
So the question is, why would you want to do that? The purpose of a duplicate target is to 1) point the OP to a place where he can find the answer he needs, 2) point potential answerers to a place where their contribution is appreciated, 3) provide a rationale for the question being closed and 4) statistics and metrics for the usage and closings on SE sites.
For #3, one duplicate target is absolutely sufficient. If you have links at hand which would help us achieving #1 and #2, just post them manually in a comment to the question. This also gives you the freedom to point out questions which are not duplicates at all, but will enhance understanding of the topic. This may be overlooked by people taking a glance at the question, but the ones who really need the info will probably read it. Having the system somehow recognize them as an "official duplicate" doesn't really help with any of these. #4 is for the benefit of the SE team. If they don't need this information, that's for them to decide.
If the question has so many comments that the one about the related questions is going to be hidden and nobody will see it, flag the comments for a mod to clean up. You might want to make it an "other" type with mentioning why you need a cleanup such that the last comment becomes visible.