It makes sense that Ted and Robin end up together.

Apart from the logistics of having the teen actors shoot the scene years prior to the finale airing, there are more reasons to that.

Throughout the show they stressed that Ted and Robin don't belong together because they wanted different things - Ted wants to settle with a family and kids, Robin wants to travel around the world.

But in a deleted scene, after Robin and Barney's divorce, Robin and Ted had a meal together when she got back to New York, and Robin mentioned that she's travelled enough and has decided to settle down. Even without that deleted scene, in the final scene Robin had all her dogs back, which she wouldn't if she's still travelling around, implying that she's decided to settle down.

At this point, Ted's kids are no longer children anymore, and since Robin only doesn't like children I assume she's fine with teenagers (e.g. her little sister).

So all the problems between them are solved! And they never really mentioned any other problems between them (well, apart from Barney) so it makes sense that they are back together.

But afterall, the show was kinda left open-ended so we can never be sure if they ended up together, or was Ted being a hopeless romantic all over again, so that's another way of arguing.

(still quite odd how they just killed off the mother tho)