Having never done it your way, I can't imagine why anyone would do it through pdf.
I have complete control over position, color bars, orientation and everything in InDesign, why add the extra step of making a pdf?
What am I missing?
Some users indeed complain that they're unable to print properly from InDesign after switching to a different printer, or updating printer drivers, or updating the operating system, etc.
In short, if you do experience this issue, then it's a bug in either InDesign or the printer driver. The unfortunate workaround is to create a PDF first, then print it. I agree that this extra step is ridiculous.
You can try to report this bug to both Adobe and the printer manufacturer and see if they're ready to fix it.