Call them. I've read the same anecdotes you have, and I've never encountered an assertion that the agent was not willing to honor the 15% online booking bonus if it's not possible to accomplish it online.

As for your mother's 99,000 miles, they are probably of no help. HOWEVER: Standard awards are very expensive; is 99,000 points enough for a saver award? (Or for a one way saver award? Note that you can book two one way awards for the same miles cost as a round trip. So you could book saver for outbound and standard for return, or vice versa.) Anyway, you could book a standard from your account and waitlist a saver from hers, and if the saver clears, cancel the standard. As I understand it, you couldn't do this if the miles came from the same account, but you might get away with it if they come from different accounts.

Disclaimer: I have no direct experience with this, so it may not work, and it's possible that SQ would detect the double booking and cancel one or both of them. One thing you could try is booking a standard award for one day and waitlist a saver for the day after or the day before, which is absolutely allowed. Or even on the same day if there are multiple flights. See here.