I have seen many examples, Harvard Mark 1, Manchester Mark 1, Colossus Mark 1 and 2. It is possible that this is a very obvious thing for native English speakers, but not entirely for me. Was this an old custom? Who started it? Why did it not continue afterwards?
Was this an old custom?
this word has fallen into disuse, or it has at least fallen out of vogue. In the context of computing at least, the word Mark followed by a Roman (or sometimes Arabic) numeral has fallen into disuse as a versioning scheme. And given the word's many uses and meanings, it's not surprising that this use is unfamiliar to you.
But "mark" really is just another word for "version", or "revision".
Who started it? Why it did not continue afterwards?
For the answer to these questions, better see the link https://english.stackexchange.com/questions/83548/mark-in-generational-naming-of-products
As mentioned in the comments, “Mark” here is used in a similar sense to “version”. The name of the computer is the first word in the designation (“Harvard”, “Manchester”, “Colossus”); then follows the version, or revision — “Harvard Mark 1” is the first Harvard computer, etc. Note that in some cases this designation is used even though there was no “Mark 2” (or “Mark II”): for example, the Manchester Mark 1 was followed by the Ferranti Mark 1. In some cases, the “Manchester Mark 1”-style name wasn’t the official name (the Manchester Mark 1 was the Manchester Automatic Digital Machine), but computers were so rare at the time this naming practice was common that people simply referred to computers by their location.
The practice of using “Mark” to identify computer revisions didn’t last long, and you’ve listed most of the models which are remembered in this way; I get the impression this was only used in the 1940s.
It's basicly a variant designation. The custom is originated with English military and describes a variant of some equipment as marking for (often) otherwise not distinguished items. As many other conventions it did spread from military use over to civilian engineering, like with railroad manufacturers naming improved wagoons as Mk2/3/4... In the mid 20th century it reached adbertisement and official naming, with a 'feeling' much like todays version numbering hype - like eating 2.0, Industry 4.0 and so on.
Modern day equivalent (as used in the US) would be 'Model'.