For the sake of discussion assume that I was a grad student in department A and the other areas were B and C.
1) I got my PhD in IDS and my dissertation focus was at the intersection of three different areas.
I think, I was successful in pursuing the committee member to hand me over a PhD (rather quickly) by formulating the question of the dissertation as "solving problems in B and C areas using awesome-expertise in area A".
The trick worked because it contributed to human knowledge(and hence published papers) but also because the dissertation "spoke" their language. This language took me a long way because the faculty was able to see my contributions even though some of them were not familiar with areas B and C. I am confident that I wouldn't had gotten my PhD if I were to formulate the work the other way around.
2) For your academic career I hope this will turn out to be good (since every one or many want to do IDS). This is not to say that doing IDS allows one to get a faculty position (which I still haven't) quickly. That is because getting a faculty position in a department while doing IDS has its own sets of challenges.
I got my PhD in department A and would like my faculty position to be in department A as well; since I am the most expert in this area and will be able to teach courses etc.
Departments want to have IDS people. However, they do not know how to assess them in their scientific merit. So a department A would be impressed by my publication record and will call me for an interview. But most of the faculty is a specialist in one core-area, which is common in my sub-fields. Therefore, most of the hiring committee members would know one of your area but not others. Hence would be less inclined to acknowledge your contributions in other areas (or at least the fact that it is difficult to do IDS because they themselves have never done it; other would be cocky because they might have tried it and failed in doing this so would come and bash you to feel good)
Most of the members would complain that you didn't talk about areas A-1, A-2 etc. Well, I would if I were also not concentrating on areas B-2,C3,4 AND A-3 & A-4. I am sure these members go back for the meetings and bash my work in the same way.
For the time being I am presenting my self as a faculty candidate by using the strategy that I used for my dissertation. I hope it works. Time will tell.
p.s. In case you are wondering why "the bastard child". This is because everyone want to do IDS and want to hire IDS people. But no one want to take the responsibility (credit/discredit) of the newly found research areas.