The author told The Quietus that the broadcaster did not mind him inserting aspects of his own multiverse into the book, which was published in October.
Moorcock said: "The only real problem with Cardiff, as we call the BBC... was, I wanted Amy to have her own room in the Tardis, so I can describe her getting up in the morning and hearing something going on in the main Tardis bit, you know, and coming in to breakfast, or whatever it was.
"They didn't like that, and I think it's because they've got story plans that might not fit. I wanted to have Captain Jack in, but they didn't want me to, again because they kind of save these characters up for a specific purpose.
"It's not really a strong idea they've got, but they know they might want to use it in a certain way. But that's what you get if you do a job for hire."
He added: "I've had fun with it. But in a way it enabled me to reclaim stuff that had filtered into Doctor Who from stuff that I'd originally done. That happens when you're my age and working in popular fiction; it spreads through the genre.
"But Doctor Who is a comedy; it's predominantly comedy, but with a big idea, and that's what I like about Doctor Who. When it's at its best it seems to have both those angles."