Fully agree. Guess the determinant is how much you can "avoid" dealing with the OTA in the event that something goes wrong.

For example, I only book SIN-KUL and KUL-SIN as one-ways. If something is wrong (eg. flight cancellation, and they end up putting me on an alternative inconvenient timing) I can call up MH anytime as soon as I receive the cancellation email, and they'd just put me on another flight without any fees.

Compared to when booking on CheapTickets (yes, I've no issues calling them out) they absolutely REFUSED to move me, insisting that MH would charge an amendment fee if the alternative flight was within 3 hours. This was after my telling them that I had called MH and they confirmed there was no amendment fee because it's due to their own cancellation, even conveyed to them a specific code that MH had asked all OTAs to use to process any amendments due to cancellations. CheapTickets customer service is terrible... you take a long time to get through... and they refused to get on a conference call with MH, and terminated my call after 30 mins. In the end, I waited until 24 hours before the flight, when it went under MH's own control, called MH directly, and it was amended with no further hassle.

Yes CheapTickets was like 7-10% cheaper for the SIN-KUL and KUL-SIN routes (I used was, because it's no longer). But the hassle of calling them in advance made me considerably stressed. So if you can wait until 24 hours prior to departure to call MH directly, this may still provide you with the OTA savings that you're after. It's possible for my routings because there are multiple flights per day between KUL and SIN, and they rarely ever sell out... but for other long-haul destinations where there's only one flight a day, one may not want to play roulette with an OTA.