What do you expect to get for the case you've listed? This falls outside any of the cases you've described above - see I know what I mean. Why don't you?. If you expect to get

zero

<begin block>

one
two

<end block>

    three
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which cleans out blank lines but keeps the spaces before three, you can use a non-capturing group (?:...) combined with the ? quantifier to make the whitespace matching conditional:

 echo -e 'zero\none\ntwo    three' | perl -0777 -wpe 's{\s*(one\ntwo)(?:\s*^)?( *)}{\n\n<begin block>\n\n$1\n\n<end block>\n\n$2}m'