I think it is a matter of comment sense. Any clearance must be unambiguous and contain the specific. If the published approach is to be modified then this should be by agreement but following a request from the pilot. ATC can of course make an offer but this must be accepted by the pilot. Therefore if the initial clearance is via the IAF then this should be continued unless the later clearance specifies not: i.e. "cleared to route direct" to a specific point. The oldest rule is, of course, ask if if the clearance is not clear.