I agree that this is a problem Apple needs to solve since more companies are beginning to use Apple devices.
I had a work iPad. My AppleID is associated with my work email. I subscribed to Wall Street Journal, Fast Company, etc. Now I've switched from a Galaxy to an iPhone... but I'll have to use my work Apple ID to keep all of my purchases, like downloaded magazines. God forbid I ever branch off and start my own company. Thankfully, I used the Kindle app instead of iBooks (and Amazon mp3 for music) and can easily download books with my notes regardless of the Apple ID associated with them. Thank you, Amazon, for remaining a company that has always put consumers first.
I'm assuming that there MUST be a workaround-- because that would just be logical for a company that is growing with it's formely young, now professional base-- so I will keep looking. But, really, I shouldn't have to dig this much.