I understand the barrel extension is separate from the barrel.
Do barrels & extensions come as a set when a barrel is
purchased, and how does one get the barrel & extension
lined up properly when they have to be assembled, i.e. buy
an M4 extension to replace a standard extension?

Most new barrels come with the extension preinstalled.  Unless you are talking about buying a blank barrel. Those come in what would be considered a "white" form.  The bore and chamber would have to be cut, and the extension would have to be installed.

Not sure on the extension swap.  Someone will be along to inform us both.

Ive asked this before.  I got a general cringe even from experienced machinists and gunsmiths like Mongo.  Its almost impossible to change the extension once the barrel has been indexed and all parts drilled.  Its much cheaper and easier to just buy a whole new barrel than to mess with it (youd have to find a machinist desperate for work to actually attempt it).  The extension is installed before the index pin, gas port, etc are drilled in production.  Theyre all determined by the orientation of the extension itself.  

Quoted: Ive asked this before.  I got a general cringe even from experienced machinists and gunsmiths like Mongo.  Its almost impossible to change the extension once the barrel has been indexed and all parts drilled.  Its much cheaper and easier to just buy a whole new barrel than to mess with it (youd have to find a machinist desperate for work to actually attempt it).  The extension is installed before the index pin, gas port, etc are drilled in production.  Theyre all determined by the orientation of the extension itself.

What he said. When you order an AR-15 barrel you get a complete barrel, which includes the barrel extension, professionally installed. None of us "AR builders" EVER install or change a barrel extension.

Quoted: How does one get the barrel & extension lined up properly when they have to be assembled, i.e. buy an M4 extension to replace a standard extension?

Read this thread, and you'll understand the complexities of trying to swap barrel extensions:

www.ar15.com/forums/topic.html?b=3&f=4&t=247052

Then you'll see why 99% of the time it is best to buy the barrel with the correct barrel extension already attached.

Thank you, Gentlemen. I was curious as to why and the difficulty of changing
barrel extensions, having seen extensions for sale. Your shared info has shown
this is something to not do. Thanks again.