You've hit all the tools I'm familiar with. Well done! PDF Arranger is a fantastic tool. I'm very happy the developers picked up where PDFshuffler left off. I use Xournal frequently for highlighting and annotating. LibreOffice Draw is best for fixing or editing elements within a PDF page, in my limited experience.
For those who don't like and wish to steer clear of flatpaks, there are binary releases of PDF Arranger available for many distributions:
I switched my Mom over to Linux almost ten years ago when Vista ended mainstream support. She's never looked back.
I had been trying since the early 2000's, when I abandoned Windows forever after one BSOD too many. The showstopper was Quicken (*ugh*). That was non-negotiable. So I kept trying her quicken edition via WINE every year or so.
Push came to shove in Summer 2012 after Vista went EOL. I insisted it was time to change as running unsupported Windows is just too dangerous. I suggested her two best options were to get an Apple so she could (for a price) have ready local support, or we could try upgrading to Linux at no cost and little risk. I did leave the window open for Windows, but let her know I wouldn't be able to help much as I hadn't used it for almost a decade, and hadn't used Win7 at all. She liked the Apples, but felt a little snubbed by the Apple Store staff at the time (she was 76 years old) and was reluctant to spend the large amount of money they wanted. So Linux it was!
I installed whatever Xubuntu was current at the time onto her fairly-high-spec tower PC. Everything just worked, no surprise. I turned her loose on it and she loved it. Most everything was where she expected it to be and worked the way she was used to, and it all worked faster too. Her ancient Quicken even finally worked with the latest WINE, except for the connectivity features (which she never used, and that I consider phone-home anti-features).
A few days later we also upgraded her older Dell "kitchen computer" to Xubuntu Linux. Again everything just worked, and she loved how much faster it was. I set up both machines so I could administer them remotely.
Today both PCs have been replaced with modern mini form factor machines. She's still running the latest Xubuntu on both and still loving it. She is the envy of all her octogenarian friends!