Yes that is how it works. But when the new mturk changes happened last year they change something so that panda's and searches won't interfere with each other and cause PRE's. I found this out last year around August by accident. I am sure if running too many searches at once will cause PRE's but it seems to have it's own limits now.
So if you run a search on a batch that runs all day then yes you would be correct that you'll be getting more PRE's which would defeat the purpose because it would be running panda's all the time interfering with other panda's. Now I have one Panda Crazy window on my second computer that runs only searches for stuff that comes out once or twice a day sometimes like C-sats, pinterest or ipsoft. At the same time I have Hit Catcher run on my main computer at a speed of 1000ms on a batch that runs all day. The PRE's on Panda Crazy shows 0. Hit Catcher shows less than 50 but I've been trying to catch some surverys today too. I even tested Panda Crazy running only searches at 700ms and still get no PRE's or very few.
Of course when the searches find hits than the PRE's will start causing problems and it's best to turn off Panda's at that time if you can. Many times I don't and understand I might get less.