Inertia - for your issue - when you lodge a tax return and are entitled to top ups of ftb - the info is sent to ATO. they are given a "pay by" date - a date by which they have to include it in your tax return or return it to FAO. this is the date that is seen on the FAO system - unless it has a payment id number, it's only a "should be paid" scenario. if it isn't paid by that date, it is returned to FAO within a few days and then sent out to you.

TM - if you overestimated and your combined income put your payments above the threshold for max payment (around 42k from memory) your ftb would have been reduced and yes, you'll get a top up plus the pro-rata supplements. if your combined estimate was less than that amount you would have been getting max rate ftba anyway. you may get an ftbb top up.