Yup, it'll shift up for ya but it will also let you downshift as far as you like whether good or bad.
I can't say for certain if it applies as I've never driven the PT with Auto-Stick but my Dad's Prowler would sometimes lag a little when I was downshifting and thinking I hadn't pushed it over far enough I'd hit it again and it'd bog waaaay down like ya said.
I think the gear indicator is in a more prominent place in the PT so it shouldn't be hard to get in the habit of checking it before you bog it down. Think it's just one of those things ya have to get accustomed too.
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