[heraclius]

It’s not that Malaysia isn’t a threat (there has been sabre-rattling too, e.g. in 1991 when the army was mobilised in response to a Malaysian exercise)—just that it’s not only or most important one. Merely geographically Indonesia is probably in a broadly comparable position to try to blockade Singapore to that of Malaysia. There are fewer e.g. Javanese citizens of Singapore, and many Indonesians assimilated to a Malay community principally associated with Malaysia and not Indonesia if anything, so fears of dual loyalty do not tend to focus on Indonesia; for example many Malays will have Javanese ancestry.

Changi is not, as you point out, really a big US base, but I imagine that putting strategically important thingums for the US Navy at risk would not be regarded well in DC which, (inter alia!), would deter Malaysia and Indonesia. It would also hurt US economic interests regardless because of the port and various investments, so I suppose the US Navy might not even be terribly important.