Since my quote from the rule book is being quoted, I'll reply:
No way is that paragraph going to be interpreted as allowing any mechanical (or other) smoothing of the as cast/delivered interior of combustion chamber, ports, or intake manifold runners/interior, beyond that (ie 1" port matching) specifically allowed.
There was a well publicized DSQ of a limited prep prod winner a few years ago based on what I believe were pretty minor "cleanup" marks on the manifold interior (IIRC).
To stay legal in limited prep (ie L2) Prod you had better not clean things in those areas with anything that will leave marks, which I believe is well understood by the OP, thus his question. Going at things aggressively with a rotary wire brush, for instance, would be very dangerous wrt legality.
I was quoting that passage wrt shot peening con rods, which I think is well within the intent and likely interpretation of that clause.