It might not be easy now, but obviously as the tools mature and more programs support epub as a format it'll become pretty simple to create working trouble free files. It's already pretty easy now with just a few tweaks needed.
I'd rather go the extra mile now, rather than be left with hundreds of lrf files that can't be read on my next device.
Of course I'm going the html to epub/lrf route anyway so re-creating any troublesome epub files in the future is a simple as using the "Convert E-book" option in Calibre.
For most ebooks I use Book Designer to edit and then export as html to Calibre (after some tidying up). I can then create either an epub OR an lrf file.
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