I don't know if there's any of the regular posters here who listen to lots of modern jazz or would consider themselves aficionados. Failing that, and on the basis I gave this a top score and do own a bit of later jazz I'll have a crack at answering the question though the answer is probably no different to other genres but I'll come back to that.
I think I mentioned Don Ellis in my review but there was also another couple of more recent artists I also thought about when I was mentally trawling my record collection, them being Brad Mehidau and the Esbjorn Svensson Trio but you've mentioned GoGo Penguin and literally in the last few weeks I've got into them a bit off the back of going down a rathole about recording of drums in relation to one of my 96 picks to come in the Rock and Roll Evolution thread. My caveat is that I've only really listened to v2.0 to any great extent so if that's not indicative of their wider catalogue I might be miles off base.
Anyway I think you'd call GoGo Penguin very jazz influenced but as you say there's other stuff going on. Be that as it may what I like about both Time Out and v2.0 are ultimately the same thing: that they groove. They groove in pretty different ways but both do it without you having to 'know' stuff to enjoy them.
Two things I particularly like about Time Out is that it kind of shows you what its doing without forcing it down your throat so it grooves in a relaxed way. Also the way Paul Desmond's sax improvisations float over isn't an nice to have for me it's integral to the songs and makes them imo more accessible, when he plays behind the beat it has a little bit of swing and manages to accentuate the groove rather than take from it.
In contrast I think v2.0 is more about a metronomic groove, there's no swinging, no lilt to the rhythm, it locks in the groove and then adds stuff to it. So a track like Garden Dog Barbecue grooves harder and faster and I like it a lot and certainly it sounds more 'modern'. Even though it's all (I think?) human made music, it has that precision repetition and more of a minimalist vibe that makes it sound like electronic music even when technically it's not. When I read about the drums on it I think they composed them using software and then recorded them all pretty much through performance? I was going to say very unjazz like, but I'm not sure that's 100% true. A track like To Drown in You has a much more austere vibe than the Time Out tracks and I wonder if that is what makes it feel more modern? Tangentially I wonder what
@RobMCFC would make of them?
But I don't think it's an either/or. If I feel like I want something that I can skip to then it'll be the Dave Brubeck album and if I want something a bit more hardcore and metronomic that I can really get down into, then I can listen to v2.0. Both are propelled by their rhythms but can serve different moods and times and places.
In terms of a link between the two, from my limited knowledge I would say someone like the Esbjorn Svensson Trio who I think are definitely considered jazz are a band who are relatable to from both ends. A track (and album too) that feels like a link to me would be Strange Place For Snow - from the bits of GoGo Penguin i've listen too, EST would be their full on jazz cousins.
Ultimately whether the likes of EST or GoGo Penguin owe a debt to the Dave Brubeck Quartet and/or have in some way overtaken is irrelevant to me if they are all enjoyable to listen to. The Jerry Lee Lewis album reviewed pretty well on here despite it being a template for rock and roll that was 'superseded' in many different ways but people found virtues in it. I think some people tend towards being restless souls who want to see progress and some of us are a bit conservative and like stuff that feels timeless to them, but most of us vary that view as the mood takes them.
Edit: I've just checked and Strange Place For Snow is nearly 25 years old! I'm becoming an FOC.
Whilst we're on the subject have I imagined it or have we discussed The Bad Plus on here before?