Tejas Mehta - thanks for the feedback, this is briliiant, very useful.
From testing the commandlet on a tenancy that does not have the functionality enabled, it will immediately proceed to the next line. When I tested it the following day (today), when it was enabled, it took a bit longer to think about it and process the request (so I guess that can be a way to check if it is enabled yet or not). It would be great if there was some confirmation text to show that the request is being executed or processed though, it would make it a bit more obvious.
Back to my questions...
The homepage for the sites I have tested this on our modern pages. The modern experience has been on the site collections for a while and the site collections might have one or more modern pages already and the transition to this new look and feel is already well underway (the groupification is the last step).
I can understand a homepage being created and set when the flag is not present (and I take on board your comments), but I think there are two reasons why someone might want to use the keep homepage flag:
1) They have a homepage which they love and it has all of the settings / WebParts and content on it that they need (modern or otherwise). Flipping back to a different one without that content can be confusing for both the users and the admins of the site.
2) They want to create the homepage themselves as a secondary step with the correct WebParts as part of the upgrade process (with a predefined pnp template, via a script). Otherwise you might have gone from a fully envisaged beautiful homepage to one with three quick links and a news Web Part (obviously the site admins can change this in the UI).
Obviously you could do that after the sites have finished being processed, but due to the asynchronous nature of the process, it's hard to know when the process has completely finished (so you would have an interim homepage until this gets sorted).
Now what would be amazing, along with the logo switch, is a way to throw a PnP template into the mix to define the shape and create the homepage once the process has finished.
Keep up the great work, I hope this stuff doesn't sound like undue criticism, but more like things that could make it even better :)