There are pros and cons on this issue. Sometimes folks need a quick result and do not have the time to look for better alternatives. Other times is appears there is no alternative. The latter includes the case of making cropping permanent (see below, I found it). It used to be that using Reduce File Size would remove the area outside the crop, but that is no longer the case. There are also preflight scripts or JavaScripts for many needs, but they are often hard to find. The article on refrying is interesting and it points out some of the drawbacks and I thank you for posting (a good read), but it primarily points to the pitfalls if a refry is done so one is aware of the expectations. I have found that there is a way to delete cropped info permanently, though I have not tried it yet. Under Tools>Protection>Remove Hidden Information you get a whole analysis of all of the hidden info. You can then select the parts to accept. For the issue of converting a booklet to single pages, you could crop the left, remove the hidden info, and save to left.pdf. Then reload the original file and crop the right side, remove, and save. Then combine them and reorder the pages. It took a google search to find this option that I had missed all this time! So there is probably a way to do most of the things for fixing parts of a PDF, but for many the time to hunt for a solution is just not acceptable in their workflow and the trade-off of a refry is worth the time savings.
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