Why was Canon’s first EOS Digital Rebel called the 300D instead of the 100D?

Only the person(s) at Canon who made the decision at the time could say definitively. For anyone else, it's just a guess. But there may be a likely scenario.

There had already been an EOS 100 camera. It was a 35mm film camera introduced in 1991 and marketed in North America as the EOS Elan. It was a model aimed at advanced amateur photographers. Unfortunately, the internal connection between the main control dial and the electrical switches moved by the dial was prone to breaking in the EOS 100. At the dawn of the digital DSLR age it was probably thought that an EOS 100D would be too easily confused with the EOS 100, which had a couple of known manufacturing issues and was discontinued in 1995.

The EOS 100 was likely still viewed in a negative light by more than a few Canon customers when the first Digital Rebel was introduced. There were still used EOS 100 cameras on the market for sale very cheaply over a decade after it was discontinued (and several years after the 300D had taken the world by storm!) - mainly because no one wanted them. Canon probably wanted to avoid the risk of anyone associating their new consumer DSLR with one of the biggest clunkers in the entire line of EOS film cameras.

As to why they didn't start with the EOS 200D your guess is as good as mine, since to the best of my knowledge there has never been an EOS 200.

The EOS 300, on the other hand, was a more recent and very successful film camera at the time the 300D was introduced to the market. Canon likely welcomed an association of their new consumer DSLR, the Digital Rebel/300D, with the EOS 300 film camera.