The problem with that queue is that you'll have no germ to make the occasional scout/coloniser as you won't have any germ.

I put in a couple of mines once the initial factories are built and then a big slot of factories again.

So would you advise something like:

10 factories
10 mines
1 terraform
1000 factories
1000 mines
100 terraform
5 defenses

Or is it better to manually switch planets from "developing" to "production" style queues?

Remember also that "auto" never builds above the needs of current pop, so no worries with pop holds either. And of course it's easy to intersperse more urgent orders in between the "auto" ones, which will still be there the next turn when the urgent ones are done. Rolling Eyes