#1 If this were something huge like a Galaxy, Nebula, or Ambassador-class ship, I wouldn't think anything of it. What I am objecting to is proportionality.
The
Sovereign-class is almost 90% the volume of an
Ambassador-class and still pretty damn big, being almost four times the size of an
Intrepid and over eleven times larger than
Constitution. We don't have many hard facts about the
Lamarr-class but we know it has 29 decks to the
Sovereign's 24 and may be slightly longer, likely giving it a larger overall volume. We also know it's a new, experimental science ship, which makes it more likely to have unusual features compared to a more conservative "standard" ship class like the
Sovereign. A giant cetacean ops section attached to stellar cartography or advanced navigation and propulsion research, exactly as we see in
Prodigy, makes sense in this context. The ship is optimised for its intended function; you might as well complain about why the
Akira-class has so many photon torpedo launchers when other ships do just fine with far fewer.
#2 If Voyager-A cannot saucer separate, fair enough, but again, the whole point of the engineering hull is to keep the warp core away from the saucer section. It just seems weird for it to be in the saucer.
You keep banging this drum. Why exactly does the warp core have to be kept away from the saucer section? It makes some sense in the days of the
Constitution-class when warp cores were too large and complex to eject in an emergency and you had to get the crew to safety somehow, but by the mid-to-late 24th century ejectable cores are standard. It's not like the cores release dangerous radiation – we see people happily working alongside them day in day out with just a standard uniform. We've also seen a huge number of ships active in the 24th century that definitely have no separation capability:
Akira, Centaur, Constellation, Danube, Defiant, Echelon, Freedom, Gagarin, Intrepid, Miranda, Norway, Nova, Reliant, Sabre, Sagan. It's debatable for several others. They also all have escape pods so it's not like the crew are consigned to death the moment the warp core hiccups.
In fact I'd argue that the reason secondary hulls began to house the warp core was less "to keep it away from the saucer" and simply "because it meant that it was closer to the nacelles, and freed up more space in the saucer for crew facilities". Neither of which is a fundamental requirement.
#3 In all of Star Trek, I have never heard of arboreal ops, what is that even supposed to be?
As I've already said, I was being facetious. It's obviously a joke relating to you being so hung up on cetacean ops. It was either go with this or talk about them rechristening the
Voyager-A to be yet another
Ent-erprise.
#5 There'd be very specific reason to put a forest on a Starship, not just a flippant "why not?" We know Starship life support systems, biological research labs, and recreational facilities do not require a forest to be onboard, so why on the Voyager-A? I think it's a reasonable question.
We know that the
Constitution II-class and the
Galaxy-class have internal arboretums as standard so clearly this is not
that unusual, even for smaller and older ships. While life support, biological research labs, and recreational facilities do not
require a forest, true, it may be desirable for certain mission profiles or specific crew activities – and as already mentioned, we know the
Lamarr-class is a new experimental science ship, which means it's going to have unusual requirements or features compared to most starships. The
Crossfield-class, the "new large experimental science ships" of their day, are shown to feature a huge "cultivation bay" for harvesting fungal spores.
Also – starship MSDs are full of things that turn out to not really be there, or that are represented in oddly prominent ways. The
Enterprise-D doesn't really contain a giant rubber duck, a Porsche, a Douglas DC-3 plane, or a shuttlecraft designed to look like Snoopy. Some versions of the
Sovereign-class MSD, including one shared by Rick Sternbach on his Facebook page as the "definitive" version, include a TARDIS – which would certainly go some way to addressing how to deal with it being so much smaller than a
Galaxy-class.