You mostly restated what I said. If you run out of space, upgrade labs. Otherwise they suck. Its the worst way to improve research.
But my point is that you will always be out of space. Colonists just don't grow that fast. You will inevitably be upgrading labs. If you don't have better lab techs, you're losing research because you can't upgrade. If you're waiting for pops to grow, or clearing blockers, you're spending inefficiently.
As for local tech bonuses, aside from IIRC a certain unique building, there's 3: research assist, orbital bonus, and governor. However, two of those bonuses use the same resource (leader slots), and two of them can made not local easily enough. Yes, there are planet based bonuses but honestly they're only going to account for a drop in the bucket even if you focus on them. This is coming from someone who filled a max sized world with the best physics labs available, and the unique lab, and then stacked every possible research bonus on that one planet (including the space mall for happiness). I wasted so many minerals doing that and the gains felt very minor compared to what my generalized worlds were yielding for much less cost.
AFAIK there's no unique lab building for a planet alone. You're maybe thinking of the Research Institute which gives 5/5/5 tech, and +10% to your empire. There's a spaceport upgrade that gives +10% research, but of course you can and should build that everywhere you have any significant number of labs.
But anyway, calling localized bonuses a "drop in the buckets" is absurd. Assist Research is by far the largest bonus available in the game. A 5-star scientist gives +25% or +50% output (more if you have racial traits/policies for higher levels). Sure, it uses a leader slot. But there isn't a better use of a leader slot than a scientist running assist research. No other leader bonus comes close that much research output - or anything output, really. There's a Food leader, and a Slave leader for minerals+food from slaves. Not a lot of options.
Was it useful for you to stack that much research on one planet? We don't know, because you didn't say anything besides, "idk, feelsbadman." Do the numbers. What did the planet produce before you upgraded it, how long did you spend upgrading it, what did it cost, and what did it produce afterwards? What techs did you research with it and how much sooner did they become available? What would you have spent the minerals on if you hadn't done that? If the answer is "maxing out my fleet capacity" then you should have already done that anyway.
As for your point about the research bonus of tech, you're missing the point. The game is designed so that you quickly fill out "core" techs like your main weapons path and basic utility upgrades and then past that you have to go after sidegrades and diminishing gains. The fleet size modifiers are great, yeah, except that expanding empires tend to run way below their fleet limit and all those minerals and energy you've been dumping into upgraded labs a smart player would be buying corvettes and spaceports.
Nah, you're assuming the opposite of what I'm doing. The player should always fill out their fleet capacity first. You don't invest in research at all if you don't have a full fleet. The cost of maxing your fleet capacity is generally insignificant compared to investing in infrastructure. The cost of a corvette is insignificant compared to building/upgrading.
Sure, you can use your research to rush down a weapons path, but most smart players will quickly get decently far down 1 weapon, 1 defense and reactors. On top of that improved weapons increase BOTH the cost and maintenance of a ship, which means that until you hit your fleet limit higher tech weapons = smaller fleet.
Nobody is talking about "rushing" down a weapons path. The point is that tech matters. It's not just sidegrades. Sure, higher tech weapons cost more. Who cares? Higher tech also produces more money. The point is that being 10 techs behind is a real disadvantage, not an imaginary one.
All of this means that, sure, a high tech empire has an advantage over a low tech empire. But between the smaller fleet and the fact that many advantages that improve tech are trade offs with things that produce minerals and fleet limit (see: having a small empire, upgrading your labs instead of your starports), it all evens out close enough that it is a secondary deciding factor to fleet size, alliances, and rock paper scissors. Sure, all things being even research will make the difference. But honestly I would say the bigger advantage of research is the ability to shift your position on the rock paper scissors.
Again, what is with this "smaller fleet" idea? You always keep your fleet size at max. Anything else is goofy.