1. If you open an existing PDF with PDF Clerk, the settings in “Display boxes inspector” cannot be modified.
The workaround is to create a new PDF Clerk Document and import the required PDF into it.
I can’t replicate this. Are you perhaps working on encrypted documents? (Documents you had to first unlock with a password? If not, then I think you are trying to alter the display boxes while showing an imposition. To do that you have to switch the page list to the imposed sheets tab. Then you have control over the boxes. But that won’t allow you to alter what happens at the fold.
2. The Display boxes inspector shows 2 options for changing the layout. The first is “Media box” the second is “insets from media box”.
The way to change the layout to suit saddle stitch with bleed on 3 of the outside edges (not ‘guttter’) is to alter the first x Coordinate position with Media Box. However, this change cannot be replicated throughout the remainder of the document with “Mirror on opposite pages” checked and “Apply to Selected Pages” . It does the same thing to all pages, this is after selecting the group and re-selecting the initial page and associated set of corrected values. ( all pages modified left side edge for example)
The mirror on opposite pages check box doesn’t apply to the media box options. Only to the inset boxes. So, if you want to change the using mirrored pages you’ll have to do so on the crop box, and show the document by its crop box, to get the desired results. For what you want to do, that may not be an option. I suggest you select all odd pages, change the x of the media box and apply to selected pages, then select all even pages, and change the x to the opposite amount and apply to selected pages.