Yes it's true, and it's probably the first thing that's asked about by most people watching the Tour for the 1st time. There are a couple of reasons;
1. To avoid a mad scramble by everyone to gain a second at the end and putting everyone in a dangerous situation in a pack of nearly 200 riders.
2. The difficulty of separating everyone individually to the fraction of a second. Actually this could be done today with electronic timing.
It's generally conceded that everyone finishing in a "group" will get the time of that group. Later in the mountain stages, you'll see riders split by just a few seconds and they will take that into account in the overall timing. I know, it's weird, but not when you've been watching bike racing for 35 years...it's just "normal."