I think it's most appropriate to post my response here vs. the composition sub-forum copy of this question, given what I have learned about the instrument from the maker of the one I own. And yes, I too noticed the issue you mentioned, but when I use the lowest octave of the marimba it is usually in conjunction with related instruments that also have "interesting" tonal and harmonic behavior down there.
Basically, it is the bars themselves that must be tuned a certain way, and this is the most expensive part of making a marimba. Furthermore, people have different tastes and needs, so the maker of my marimba (withholding the name in case it is inappropriate to mention that here, especially given that VSL sampled a Yamaha model) offers three different versions of bar-tuning, plus 440 vs 442 etc.
As you probably know, the intonation of a marimba and especially its harmonics are not constants and change during the course of playing the instrument as well as due to seasonal differences and other climate concerns. This makes it a very challenging instrument to sample consistently! I am not sure if the player rested for long periods between octaves, if the room was climate controlled, etc.
It is hard to know all the specifics, but I have noticed similar issues with other vendors' marimba libraries, and to more of an extreme such that I ended up consolidating exclusively to the Synchron Marimba. I use different mallets for low vs. middle vs. high notes anyway, and this does mitigate some of the differences as does a sensitive ear to dynamics and a lot of patience in perfecting the performance.
I bought a 4.3 octave model as I don't much care for what happens below that; I have moved away from the bass register and bass voices of quite a few instruments lately in my orchestration work, one example being bass flute, as I feel that, except for doubling, those instruments aren't as effective or distinct vs. other choices that have fewer issues in the lower range.
I'm often surprised by the improvements when I move away from my original concepts of an orchestration, and I also like to "trade voices" during a phrase. But I don't yet have a full answer myself for whether the marimba can be fully tamed in every context. I'll probably have a higher awareness of this situation once I start recording my own marimba vs. using the libraries available. After all, the libraries are recorded in a methodical way, whereas most music has a distribution of notes that are comparatively random.
One more note: is it possible to use the timbre feature to program velocity-sensitive pitch adjustments, which I think is how that feature works in Synchron Pianos?