"I align the two windows side-by-side with approximately the same width so that I can visually identify if anything is missing, line by line."
I switched from using Workflowy (never had conflicts, used on desktop and mobile every day) to Evernote as I thought it would be a better platform as it's actually being worked on and improved. But this makes me wonder if I should go back, this is the minimal expected functionality you'd expect of anything cloud based. Imagine if Google told you to bring up your two conflicting Google docs next to each other and read through line by line.
There must be a solution for this. I use Google, Workflowy, Asana, Jira, Dropbox all on multiple devices and never have any sync issues.