O.K....without getting too boring and long winded, lets use the following QUICK definitions: probable cause is when evidence shows a reasonable police officer that a crime has been or will be committed. Reasonable suspicion is when the evidence shows a reasonable police officer that a crime might have been or may be committed. Obvious difference. Reasonable suspicion allows the officer to detain in order to complete an investigation within a reasonable time. This investigation should be only to validate or negate his suspicions. Usually includes non-accusatory questions, drug dog scan, ID checks. Probable cause is necessary to make an arrest or obtain a warrant. Probable cause would mean that the evidence for arrest has already been obtained, and you are sort of screwed then.
In an airport, or any other secure area..such as military base or federal buildings that are marked secured, you agree to random searches of your person or vehicle depending on the location, by simply performing the act of entering the secure area. This is because the perceived overall safety of the public trumps the rights of the individual entering the area. Not arguing either way here.
In a airport, prior to entering the secure area, one may refuse a search, but will be asked to leave. After entering the secure area, the rules change. You are now obligated to comply to a search request. As I stated earlier, this will not be abused 99.9% of the time, and I hate that it does happen once in a while. It is usually the result of an overzealous cop or undereducated one. But the bottom line is, they can search. As far as the logic that TSA has already searched your bags, well...the LEO's love TSA about as much as FT and probably trust them less. If I were an airport cop, I would not take for granted that you were not armed just because someone at TSA said your bag was safe (sorry Bart). Most LEO's would rather not screw with the passengers as they know that they are dealing with the upper part of society at the airport and that most travelers are law-abiding citizens. Some do get bored, I guess, and you end up with the abuses you mentioned.
The depth of the search depends on the perceived crime. Like serving a search warrant, it must stay in context with the suspicion. If I am searching for a gun, looking through your wallet would be out of bounds. If I think you are an illegal alien, then it would be acceptable to check you ID's. Most of the time, if you speak to the officer like an intelligent adult, they will be less likely to run you through the mill. If a officer wanted to search me, I would ask what prompted the search and what he was looking for. If it were a gun, I would assist in opening my bags so that he would not destroy everything. They appreciate encounters that don't end with "I'll have your badge". But I would also ask for a supervisor if the search started to take too long or went beyond the scope of suspicion.
I do not know the TSA rules on inspection in secure area, but the screeners do not have powers of arrest or investigation. I would guess that they can request a rescreening of your bag, but it would make sense for them to just contact a LEO to do it.

Hope it helps and was not too long winded....it was, wasn't it?