The other answers are missing out on the key reason: licensing.

Copyright law differs between regions, and so different groups need to be paid when the video is “sold” to a customer. Before the early 2000s, this was even more the case than it is today; the US hadn’t yet tied its own definition of copyright to all its trade agreements.

End result? Selling a US DVD in Japan would have been illegal; not because of the region restrictions but because the people who had to be paid to play it in that region hadn’t been paid so the DVD was effectively a bootleg.