FedEx long way round
 

Any reason for this?

https://cimg6.ibsrv.net/gimg/pprune....4454ef8a0e.png

Looks like no Indonesian overflight clearance. The only volcanoes that have been active in Indonesia recently are Sinabung (west of Singapore) and Dukono, which is close to the track flown, so it was unlikely to be due to volcanic activity.

That route requires Indonesia clearance along certain airways after leaving SIN.

Is that a charter flight number? If so, perhaps arranged at short notice and permits weren't granted in time?

Anything beginning with a 9 is a charter/ad-hoc. It was routed this way to avoid Indonesian airspace due no overflight clearance.

Begs the question why they couldn't get an Indonesian permit. Being a charter flight, they would have had more than enough time to get one.

Plus, if they flew on either M758, M646, M761 or G580 out of SIN then they would have needed an Indonesia permit anyway.

Wrong. All these airways are under SIN WMFC FIR

flightleader - these airways may be under SIN WMFC FIR but Indonesia CAA permission is required because those airways overfly Indonesia land-mass i.e. islands.On 14 Jan 2019 an Ethiopian Airlines flight was intercepted by 2 Indonesian Air Force F16's for flying across Indonesian airspace without permission. The aircraft was initially supposed to operate from HAAB/Addis Ababa to VHHH/Hong Kong, but was modified at the last minute to route via WSSS/Singapore instead, to make a delivery of Rolls-Royce Trent 1000 engines.

The Ethiopian Airlines aircraft was intercepted forced to land at WIDD/Batam Island – which lies right in the middle of the chunk of airspace controlled by Singapore.

Would there be any difficulty / red tape in obtaining those permits?

Unless the carrier is barred from using Indonesia airspace, the process is simple. The lead time to secure is around 48hrs once all relevant documents have been provided.

Maybe weather?

Weather would not force an aircraft to avoid a whole (large) countries airspace. They had no permission. Simple as that.