Yes the rules read the same, removing an end cap and shaving a bat are both altering. The reality is that they are very different and lumping them in the same category doesn't make logical sense. With a lot of bat companies refusing to fix end caps on NR bats or on bats that are past the warranty, this is one of the times that I don't see a problem with using an "altered" bat. I don't see a logical reason to throw away a $150-$200 bat because the $10 piece of plastic that has nothing to do with performance or safety cracked or came loose.
I have never called out an opponent's bat during a game as being altered because I don't feel I could know for sure. That being said, I don't have a problem with them being lumped together for several reasons.
A, it's the rules of a game you choose to play. We're not talking about state or federal law here.
B, the temptation to go ahead and shave or endload a bat once the cap has come off is too great to assume everyone that replaced one didn't do anything while they had it open. We're talking about a community where so many people pay 25% of the cost of a bat above the price of the bat to have this done that the companies are enacting different ways to combat it. Of the people I've known with bats that lost their caps I'd guess 5 times as many came out from a poor replacement after a shave job than by themselves to be replaced as stock as possible.
C, the scenarios you discuss almost always come about after the original owner's gotten a "lifetime" of use out of the bat already or it's been sold to a second owner anyway.
D, I don't know how integral cap construction and placement is to a bat passing the standards, but I know the guys saying glue it back in and swing away don't know either.
In theory, I tend to feel like you and assume it's not that big of a deal. I also won't swing a bat I've known to be in this state in a game just to be safe. I don't want to be the guy that swings a bat I've replaced the cap on and have it fly off and put a guy's eye out.