It is pretty clear that a web server has to decode any escaped unreserved character (such as alphanums, etc.) to do the URI comparison. For example, http://www.example
tl;dr:
Decode percent-encoded unreserved characters,
keep percent-encoded reserved characters.
The URI standard is STD 66, which currently is RFC 3986.
Section 6 is about Normalization and Comparison, where section 6.2.2.2 explains what to do with percent-encoded octets:
These URIs should be normalized by decoding any percent-encoded octet that corresponds to an unreserved character […]
As explicitly stated in section 2 (bold emphasis mine):
Unreserved characters:
URIs that differ in the replacement of an unreserved character with its corresponding percent-encoded US-ASCII octet are equivalent
Reserved characters:
URIs that differ in the replacement of a reserved character with its corresponding percent-encoded octet are not equivalent.