EigenD is free, you do not pay for it. It is open source and you are very welcome to contributre to its development and add these features. Adding the functionality you want would probably not be too difficult, things like that are not intrinsic to the architecture, they are certainly not 'deep in the core programming'. I would certainly encourage you to have a go if the lack of these feautures is a serious issue for you. 'Cut and paste' and setup versioning would be nice to have, go for it.
You do seem to be under a slight misapprehension about Eigenharps. I sell them for about what the parts cost me, I don't actually make any profit selling them. Eigenharps are a passion for me, not a profit making business. EigenD had over £2M of software development prior to me releasing it under the GPL, it's a complex piece of software. I couldn't keep funding the development beyond a certain point, I don't have a bottomless pot of money, so if you find things missing that you'd like I can only encourage you to open up your development system , fire up git and get cracking, we all apreciate someone contributing and I'm sure Mark (who leads the community release) would welcome you.
If you'd like to assist with improving the documentation and don't think it is extensive enough then this is also possible, it's a Wiki and the one thing no-one likes is writing docs, so I end up keeping that up myself. If you have ideas about that and want to write some entries please get in touch with me directly.
John