Also, this seems to be the first time that Japanese Royal choose the kanjis from their classical literature[1] instead of Chinese literature.

[1] https://en.wikipedia.org/wiki/Man%27y%C5%8Dsh%C5%AB

Rei, 令, in this case means 'good, fortunate', not command.

Huh, according to Jim Breen's dictionary (http://nihongo.monash.edu/cgi-bin/wwwjdic) 'good, fortunate' is '礼' (rei). '令' (rei) is listed as 'command, decree'. The official character that is being used is '令'.

Is there some rule or convention that explains why 令 means 'good, fortunate' here? Is it due to the usage in the 7th century poetry that is referenced in the article?

Even though there's an explanation, I've seen a bunch of negative reaction to the name from Japanese people online because of the association with "command", also linking it to the current prime minister and his relatively militaristic politics.

Interesting; came across this Twitter thread with a fairly detailed analysis.

https://mobile.twitter.com/nick_kapur/status/111270395164693...

In this particular case, '令月' means[1], a good month.

https://kotobank.jp/word/%E4%BB%A4%E6%9C%88-660939

If we have to trace back even further, it can date back to the ancient Chinese classic, the Classic of Poetry, where it is being used as good/respectful:

https://baike.baidu.com/item/%E4%BB%A4%E9%97%BB%E4%BB%A4%E6%...

The namers can publicly claim it to mean one thing while privately intending to be another, of course.

In case of Chinese characters, they can be interpreted under different context, I agree.

Unless you do mind reading this is all a matter of interpretation. There is no single meaning.