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Looooonnnnngggg lines...

Wordwrap is not currently possible in Beyond Compare. I've gotten used to this. There are five things I do and a sixth that I haven't tried: 1) Wider windows help: View->OverUnderLayout
2) Rapid magnification with Shift+Ctl+Scrollwheel can zoom out to a "high altitude" view
3) High contrast color settings to help see a single letter in the line:
4) Thumbnail view at the left gives you a clue about the bigger picture. It reminds me of the sideview in video games. One tip: experment with rightclicking it and selecting enable-scrolling on large files.
5) Bottom panel To really focus on a long line, watch it in that extra bonus window at the bottom of the window.
6) You can manually set the line length but use this sparingly because it messes up some alignment performance: shorter lines. It makes the lines hard to read, too.
To manually restrict the length of a line in all HTML files use the menu: FileFormats->HTML->Conversion->CharactersPerLineLimit
Why no Wordwrap
One reason seems to be a tradeoff, opting for a more efficient algorithm that can read an entire hard drive while also, optionally reading each file line by line and each line letter by letter.
Try to remember that the panel in Beyond Compare is not optimized as a word processor, it is really just a window into the huge data manipulation that BC is keeping track of across your many files and many lines in each file. In the hundreds of lines of a given file, BC is searching character by character to find things that align.