Migrate Server 2008 R2 to Windows Server Essentials 2016

So simply ignore any explicit references to SBS like "Run BPA on the source server"? Interpret as you go?

There are BPAs for many standard windows roles. I'd run them. They to stay within the method of the document. Don't ignore steps if you can help it.

Generally agree with Cliff, though strictly speaking, the document you're using was not designed for what you're doing.  The first sentence states this:

This guide describes how to migrate from previous versions of Windows Small Business Server

(Assuming you are referring to this document https://docs.microsoft.com/en-us/windows-server-essentials/migrate/migrate-from-previous-versions-to-windows-server-essentials-or-windows-server-essentials-experience (In the future, don't just provide document titles, include or provide links so we know EXACTLY which one you're trying to follow).

There may not be an explicit document for going from Standard to Essentials because (in my experience) there isn't much demand to "downgrade" like that.  Though this is where having a deep product knowledge and experience will help and why I often say if you don't have experience, either setup a test network and try it first at least twice so you can gain some experience... or partner with a professional who possesses the knowledge you do not currently have.

It is a 12-user 2008 R2 with no chance of it ever going much past 12-users. Why would I not want to got with Essentials?

I have done a couple migrations with the document below but the source servers were SBS. Hence the question.

Here is the document I am using:
https://docs.microsoft.com/en-us/windows-server-essentials/migrate/migrate-from-previous-versions-to-windows-server-essentials-or-windows-server-essentials-experience?f=255&MSPPError=-2147217396

Not saying you wouldn't want to go with Essentials.  With 12 users, not sure why you didn't start with Essentials in 2011.  or Foundation before that.  My point is, Microsoft doesn't likely expect people to, in essence, downgrade, to essentials from a standard server so you're not necessarily likely to find official Microsoft documentation on that procedure.  You thus have to modify existing documentation for similar systems with good knowledge and experience.

Can't tell you about the past. I wasn't there. All I can tell you is where they are now and it just didn't make a lot of sense, with so few users, not to go Essentials.  

Sure looks like the same link to the same document with the exact same title :) My comment being that the title says "From Previous Versions"  not specifying SBS yet if you actually read the document it starts off with steps specific to SBS. Hence the question.