I was never really clear on which was better, but running a test on coriolis gives the opposite result:
Following this recipe you get this for a thermal mod on your bulkheads
https://eddp.co/u/PN9EWvFK
https://i.imgur.com/1AG947b.png
and this for a thermal mod on your smallest HRPs
https://eddp.co/u/CV7dPfQ3
https://i.imgur.com/LFGeD9L.png
Looks like a Thermal mod on the Reactive bulkheads is the way to go for both absolute hull and resist hull, by a pretty big margin too. Coriolis could be wrong though, wouldn't be the first time! 
I suppose it depends on the ratio of how much hull comes from the bulkheads vs. the MRPs, but it appears you're right; for the viper IV, that's the way to go. Cool. I need to update my armour to the new system anyway... guess I'll be doing to redesign work too!
On second thought, I'm going to temporarily recant my "you're right." I was planning out the changes to my build and ran into some oddities (indicating my original approach was better). I'm going to look over everything more carefully tomorrow, and make my judgment then.
Took my viper IV over to Selene Jean. For my build (one class 1 HRP, and one class 3 HRP), my original setup is definitely the superior setup- Heavy duty on the bulkheads and larger HRP(s), and thermal resist on the smallest HRP. I copied the numbers over to coriolis directly from the engineer:
thermal on the smallest HRP vs.
thermal on the on the bulkheads. Not sure if it was differences in the build you used for your test or if your numbers are wrong, but as I copied these over directly from the in-game engineer, I trust them more.
The numbers are as follows (absolute / explosive / kinetic / thermal). Note that these are without any experimental effects, since I figured they'd affect both builds comparably:
Thermal on the smallest HRP: 1519 / 2180 / 2325 / 1903
Thermal on the bulkheads: 1161 / 1819 / 1949 / 1949
As you can see, the numbers are pretty strongly in favor of the thermal resist being on the smallest HRP, and heavy duty on the rest. The thermal bulkheads gives you a small amount more effective health against thermal, but at the expense of a significant amount of the others. The absolute health being so much lower on the thermal bulkheads leaves you more open to plasma, too. Again, ymmv with different builds, but on a Viper IV with only two HRPs, the choice is clear.
