You need to 'Show Printer' in the overflow menu (3 dots in upper right).
I'm showing the Ender 3 MAX end gcode in the screen shot and it should not have a home in there. Let us know if you get it working and what you did and we will be sure to include any fixes you make in the profile.
What I am talking about with the align remaining as active is not about grouping it is about scripting or creating dynamic content. With this feature when the internal items change size or shape the align in re-applied and a complex object can be built.
Here is a great example. If you were to dig into these objects you would find that there are many aligns inside that are still active so the compound object can be resized.
And here is an animation of the aligns holding the design together as I change things.
You can see in the tree view there are lots of 'un-applied' aligns in there.
I do think there is a "power of the and" here where it could do what you expect and still be available for scripting.
Yes, that is an issue that we need to resolve. Until then, you can make the cylinder slightly larger so that the two faces, the bottom of your part and the bottom of the cylinder, are not touching. If the cylinder reaches outside of your part a little bit, it will subtract much better.
Looks like your connection to MatterHackers Community was lost, please wait while we try to reconnect.