Some of your links are very good. A lot of the content is worth reading. The issue I find is the idea that if something doesn't go into thermal shutdown, it's fine. Prior to actual overheating and shutdown, the machine does start to throttle. This can generate a lot of hiccupy behavior. If the machine is working perfectly, it won't hit this range when operated within the certified ambient temperature and humidity range.
You raise some good points so let me post some of my anecdotal experiences.
I've not experienced any hiccupy behaviour when running at 100% CPU and around 96-100 degrees C for hours on end. This is on a 2009 13" MBP C2D 2.53 GHz, a 2011 13" MBA i7 1.8 and a 2011 Mac Mini Server quad. The closest I've seen to an issue is in Handbrake itself, but this was related to a specific build where the developers forgot to allocate CPU time to the UI loop so it looked like HB was hanging and you couldn't stop or pause the encode, but it was still going, if you left the app alone.
This is nothing to do with throttling or heat though and the issue went away with the next build and wasn't present in a previous build. When a computer is truly overheating, youll know about it. Ive fried a couple of computers due to overclocking in my younger days. Youll experience very obvious instability, such as a restart or the particular application that is causing the load crashing. Then you will experience a funky noise, possibly some pretty lights if you have the computer open and a smoke display. Ive not seen any instability related due to throttling on current generation CPUs.
Will a laptop throttle back more than a desktop? Sure, but that is the trade-off for portability. Laptops are becoming stupidly powerful these days, but it would be nice to see some advances in cooling technology too. There are some methods being worked on at universities right now and they seem like science fiction so hopefully we will start seeing some of this future tech soon.
Back to whether one should be concerned about the temperatures inside a laptop: I've encoded more movies and series than I care to remember on my 2009 MBP (around 4.5 TB of mkv files in total) and it still runs quite happily today. There is, however, a real issue with this particular computer in my opinion. The heat does not impact how it works, but it impacts the user experience, because the top left corner gets hotter than I would consider to be acceptable, even if one is just editing code in Xcode and doing a build every couple of minutes. I basically had to get an external keyboard to alleviate the sweaty hands. I assure you that I am not normally a sweaty person and it wasnt comfortable after 30 minutes of typing. I also like to rest my fingers over that area. Perhaps its bad ergonomics, but damn it, thats how I do it. The 2011 MBA does not exhibit this and is comfortable to use in the same scenario.
I cannot speak for the 2011 MBP with any conviction, but I did not experience the sweaty hands problems in the couple of hours in total that I've spent mucking about with it in Apple stores. My experience also says that this isn't something solely inherent to Apple's laptops. When I was still working for a large consulting firm I had the "pleasure" of using various PC laptops, such as HPs, Dells, VAIOs and Lenovos since the company would issue a laptop and I would get a laptop from the company I was consulting to as well.
I don't know what I was doing wrong, but the HPs would get stupidly hot and in two years I had 4 replacements. Twice due to the motherboard and twice due to the hard drives. The Dells would also get hot, but I only needed one replacement due to a hard drive. I also used Sony VAIOs for two years. The first one would get ridiculously hot and the hard drive died after 4 months of use, but I never really heard the fans. I think there was a problem there since after the HDD was replaced I continued to use it for a year and the fans would work.
Unfortunately that was stolen in San Diego airport out of my hold baggage by the TSA security officials after I had checked my bag in. I am now using a brand new Sony VAIO thing that is probably the worst laptop I've ever used. It continuously spins up the fans for no reason at all and it sounds like a jumbo jet taking off. It stutters at simple tasks like hibernating or waking up or restarting or opening any application. Woe unto the user that tries to right click on a cell in Excel and choose "Format cells..." just after a spreadsheet is opened or created. It's actually comical because it takes 10 to 20 seconds, even on an empty cell. Around the 15 seconds mark Excel says it's no longer responding and the wheel starts spinning. The patient user is finally rewarded with the Format Cells dialog and it comes up quickly the second time.
It's a clunky POS, but the accountants feel they are saving money with crappy machines that slow people down, even though these people cost more per day than the machine. That's financial sense for you.
Out of all of these computers, the only one that I could use on a lap was the Lenovo. That 11 or 12 inch Lenovo was the coolest (in both definitions of the word) little PC laptop that Ive ever used.