If the majority of i5/M290 of users aren't having the issue that means the iMac they supplied me with either had a software issue (unlikely as it was fresh as a daisy, other .pdf software demonstrated the same issue, and their support were unable to find any problems with the software, and gave it the thumbs-up) or a problem with the hardware on that machine. The worry with the latter explanation is that I've seen quite a few people confirming the same problem, so Apple's lack of quality control doesn't fill me with confidence to buy another.
The way I imagine hardware problems is things beeping, screen not coming on, graphical glitches or wifi not working. Stuff like that. I don't see how they can cause performance degradation.... the only exception is the HDD, they can slow things down before breaking completely. But, then again, if you had a brand new iMac 5K, that PDF was most likely on the SSD part.
So how is it possible you have a totally different experience? I have no idea. There are many factors that could've been involved. It could be some troublesome software you installed and forgot all about it. For example, when I got my iMac, I put Sketchbook Pro on it and was surprised to see it had some graphical issues (a slightly colored square was present around the pointer) and it responded poorly to my Wacom stylus presses. I thought it was a GPU issue and attributed it to the M290x (somewhat disappointed, to be honest) until I realised that the whole issue was caused by a small app called Yoink. It had issues in this specific case and only this case - and I would never discover it without some luck. Uninstalled the app and Sketchbook Pro works perfectly.
I'm not saying you had some apps installed that caused problems, I'm just giving an example how something minor could cause a problematic issue and you could've sworn you did nothing to cause it while in fact, inadvertently, you did. I've seen it time and time again - happened to me also.
Another example - there is an entire thread of people complaining how Wacom drivers don't work well with Intuos 4/5/Pro tablets on Yosemite (running on various Macs). They claim the drivers just don't work - with some serious issues. Me? I have used two Intuos 4 tablets and an Intuos Pro tablet (at work) on several Yosemite computers, and am personally using one on two different personal Yosemite Macs and haven't encountered a single issue. Are all those people on the forums lying? No, I'm sure they are not. Are Wacom's drivers faulty? No, I don't think so.
The truth is - who knows why they are having such issues, and who knows why PDF was causing you so much trouble. But I don't think it was due to hardware issues or the power of your (former) iMac 5K. There are some mysteries we may never uncover

) For me, the iMac 5K is working great and the only issues I have are the same issues I have on my MacBook Pro and are mostly Yosemite issues.
Sorry to hear you returning your iMac and I hope you have more luck with some new Mac or PC in the future. Computers, eh?