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BeautifulSoup isn't necessary externally any more since v0.9.0. Sigil includes its own modified version of bs4. But it should affect nothing if you install it.
#1 shouldn't be necessary. Sigil won't build against a version of Python it can't use (3.4 or higher only)
#2 will probably not work (not entirely sure, but still ... wouldn't recommend it).
#3 shouldn't be any different than installing to any other prefix, I do it quite regularly.
You are launching Sigil via the bash script (installed in <install_prefix>/bin), right? Not the executable in <install_prefix>/lib/sigil/
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