The fact that it is seen as a requirement for an extension, suggests that it is a requirement during the whole validity period of the visa, and that also souns logical. The fact that it normally will not be checked again upon (re)entry does not change this.
From then onwards to the next stay it indeed can be done online. The first one of the next stay has to be done in person again, so practically for DTV all have to be done in person, except when you use an in country extension, or do the first one to soon, so your second one will be before 180 days.
Don't believe everything agents tell. There is no such thing as an implicit 90 days report. Only a TM47 accepted by immigration counts as 90 days report. If it was only about location TM30 would be sufficient. Personally I don't understand why they need a 90 day report anyway, but rules are rules, and not follow them can make it difficult.
All subsequent 90 day reports in the SAME STAY can be done online, that is the official rule. TM47 is the name of the form for 90 day reporting, same for online and in person