The hyphenation makes it clear(er) that it is [a "for each REPL"
basis], rather than [a for each "REPL basis"] (what's a "REPL
basis"?). That is, it creates a compound modifier "per REPL" that
modifies "basis," instead of letting "per" act as a modifier to the
(unintended) term "REPL basis."
To my ears, "on a per REPL basis" can only make sense if per modifies
REPL (because of the common expression "on a <> basis"),
Encyclopedia Britannica is a pretty careful writer. Here is an example
of their usage of "per-[item] basis":
Aspects of the topic per-occurrence basis are discussed in the
following places at Britannica.
http://www.britannica.com/EBchecked/topic/450964/per-occurrence-basis
That is, they have a topic called "per-occurrence basis" (for some
reason), and
they hyphenated to compound modifier.
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