I'll take a stab at this, other peoples opinions may vary but here it goes. Now I'm going to compare self built systems vs Dell etc. If you were to buy from a local mom and pop store the only real difference is that you would let them put it together instead of doing it yourself. Any and all issues that come up after in most cases would be up to you to handle either yourself or by calling the place where you had the system built.
It depends a lot on what Don means by "clone". "Clone" used to mean a clone of the IBM PC standards and Dell was considered a cloner. That definition is obsolete and has been for years. What Don means I'm not totally sure of.
There can be problems with the Mom and Pop store machines.
Some such machines are made of the cheapest components and pirated software. I've heard of hardware in the machines that could not even be identified and others glued into the sockets so you couldn't change anything without changing everything.
On the other hand a reputable store that builds using components that you specify can create a machine that is high in quality (I've had them custom built for me that way myself). By specifying the components you can make sure you don't end up with hardware that won't run upcoming software and that is easily upgradeable.
Custom built where you research each component and the machine is built to those specification in my experience gets you a stable lasting machine that can be upgraded to handle future challenges much more easily than the major brands.
Some examples of bad behaviour by the major brands that I have run across:1/ IBM - used to use custom memory which meant that they could charge more to upgrade your RAM
2/ Dell - last I checked used a ATX standard power supply -
wired backwards - so a non Dell powersupply wired in the standard way would fry your system if you didn't know better and installed a more powerful standard unit.
3/ It used to be (and may still be) standard practice to install the weakest power supply that would run the system. This of course meant any upgrade required a power supply swap.
4/ Non standard motherboards and cases so you can't just swap a standard motherboard or power supply into your major brand case. Often they are slim cases that mount the expansion cards parrallel to the mother board on a proprietary expansion card. Such motherboards are non standard and limit your replacement options rather severely and also limit what cards can be added to them.
5/ Special HD areas set aside and used to store BIOS utilities. Replace the HD or install a different OS that is not aware of that area and lose the required utilities.
6/ Proprietary controllers or cards that won't likely be supported by future OS versions as the company makes more money selling you a new computer rather than supporting you with new driver releases. My workplace was once burned that way with CD-ROM controllers that way.
7/ Integrated features that use the CPU to provide the components function by running an emulator (Winmodems, Winprinters and sound cards most commonly).
8/ Components not compatible to existing standards. Compaq used to have a custom HD. To add more HD capacity to your system you had to either replace the Compaq drive or buy another Compaq drive as they wouldn't coexist with a non Compaq HD in the system.
9/ Another Compaq. They used to use special screws to fasten the case together. Most people don't have the requisite screwdrivers to open the case and might not even be aware of any way to get them and therefore would be stuck with Compaq servicing the computer at whatever price Compaq ordained.
Some of my list above overlaps Javora which should tell you that even the big companies have issues and that those issues can be bypassed by an informed consumer either custom building or having a reputable local store custom build for you.