VES that lack of low end thump was my experience for years as well, until I did some extensive testing on loads, their effect on the output stage of a given amp, and other fun stuff. Short version is reactive loads vary wildly, and do not deliver consistent results across amps - meaning the effective eq curve will change amp to amp given the same RL!
And the long version...ultimately we created our own IR's, ones that compensate for how the amp reacts differently to the specific reactive load that will be used.
For example in a Diezel VH4 - Mesa 4x12 cab combo, the amp puts out noticeably more under 500Hz than when coupled to a Suhr reactive load. It responds differently again with a Tone King Ironman II, and sounds awful with the Two Notes stuff. So it's necessarily that the IR is lacking lows (it's just a simple eq curve after all), it's the difference in impedance curves between that particular amp-cab to the amp-RL combo contributing to the change in eq.
So we created a separate IR for every amp-cab combo in our collection, rather than just one for every speaker. The IR's are so close now that they almost phase cancel with the original mic'd cab, and all that low end chunk is retained. And it only took a few hundred hours! Hmm, I'm starting to think my obsession with tone is slightly unhealthy.