For Sigil, there's the right way, the wrong way and the Sigil way. It is always the same, so it is easy to deal with...unless you have theducks situation.
Calibre doesn't care what the structure is and doesn't change it. That can mean a little less handholding and doing for you if it is only a small mess instead of a big mess.
I agree in general about using the latest version, but handling the non-breaking spaces bounced sort of back and forth. Sigil also doesn't show invisible characters at all. At least in calibre, you can cursor along and see what is there and with some effort fiddle with them. Sigil treats them as if they don't exist.
This is mostly fine until you import some web page junk. Then it can become an issue.
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