[Galaxy S 5 Q&A, Help & Troubleshooting] qxps:
Who is not allowing you to customize it? Take the S4, all the variants except at&t and verizon can be customized, you'll just get 0x1 on knox but the device can take any kernel, recovery, rom or bootloader past a specific version. In reality, its the other way around, when you customize it, you are basically implying that you now own the device in its 100% and you are responsible for any damage to it. The only way samsung is held liable is with their recommended setup, you don't want their software and firmware? the device is yours 100% to take care of, don't bother samsung when you break it, that's not what warranty is for.

Usually, business owners grasp these decisions easier. It pretty much applies to anything else where you stray from the manufacturer's setup to a certain tolerance level. In this case, samsung's tolerance level is changing the kernel/rom for their now "enterprise" ready galaxy phones. Only samsung found a way to permanently flag you when you go astray. Low blow, but it will not make them liable for the mistakes of the minority that like to change stuff. Same goes for the carriers, they don't have to deal with you when you burn the phone because you used an overclocked kernel and they won't waste time and money supporting users running something completely different to what their techs are trained and have been documented on.

I'm not getting an S5, unless I see there will be developers making custom stuff and if there is an affordable google edition, but I do understand where they are coming from and why they implemented the knox flag.

You can't downgrade bootloaders, thus lte baseband. But, you can downgrade ROMs as long as you keep the same or a higher version of the bootloader and nearly all custom ROMs do not flash a bootloader.

Desktops are different from cell phones in nearly every way in terms of durability. And in fact, pc manufacturers may not deny you warranty on hardware by using different software, but they won't provide technical support when you decide to change the operating system and cry to them for help. And, if you return with a fried cpu or video card because you ran something different, your warranty does not exist anymore.

Another point with desktops, is that manufacturers that use windows are actually selling hardware only. Compared to android where nearly every manufacturer forks the android version to add their own ingredients like knox, sense bla bla bla and they sell you a package "hardware-software". You can't do that with windows, you can't change the windows kernel, or the ui, so the only way to void warranty is by hardware damage most of the time or by simply opening the case of the computer. Software and hardware are independent and the machines are sold on the basis that they can run x86-x64 software. Though again, tolerance for desktops, laptops and x86-64 technology is higher than phones, its more robust.

All these decisions come down to liability, manufacturers do not want to be held liable for user mistakes based on ignorance, its costly. Their sales may reduce a tad bit, but they won't have to deal with this cost. A lighter example, look at the changes google implemented in kitkat for external storage, or look how some manufacturers are moving away from sd cards and removable batteries. They are removing the liability of users purchasing cheap batteries and damaging the phone, or blaming them because they bought a cheap sd card or used improper dismounting procedures and they lost all the data.