Just because they're only building two tracks/platforms doesn't necessarily mean they're removing the space for a third track. The purpose of the third track at Aurora was to let some northbound trains terminate there and await their departure time to head back south, without obstructing the mainline, so the planned track configuration was the same as the current configuration at Unionville: side platforms on the double-tracked mainline, plus a third track along the west side of the southbound platform that dead-ends at the end of the platform. Note that this configuration does not require any additional space between the tracks on the mainline - the third track is on the west side of the southbound platform.
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There are plenty of examples where Metrolinx has future-proofed side platforms to be converted to island platforms, which is fairly easy to do since you just need to not build buildings in the way of the future track. In some of the more recent cases (Bloor, Cooksville, Guildwood, etc) they even installed tactile markings on the unused edge of the platform facing the hypothetical track.
Guildwood station, note that the westbound "side" platform has tactile markings on both sides, in case a fourth track is installed on the north side, converting it to an island platform.
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Cooksville station, note the tactile markings on the north side of the "side" platform:
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The third track at Aurora is completely unrelated to the third track further south. The provisions at Rutherford/Maple are for a passing track without a platform for the purpose of letting express trains overtake local trains, which makes no difference to the line capacity. If you don't care about average speed, you could run 15+ local trains per hour on just 2 tracks south of Aurora, which is way more than the Barrie Line would ever need. But to achieve those frequencies you'd need pretty substantial turnback capacity - a basic two-track terminal like the current one at Oshawa GO wouldn't be able to reliably terminate that many trains, so you'd need additional turnback capacity such as the proposed third track in Aurora to reduce the frequency of trains making it to the end of line. This is why some peak-period Lakeshore East trains start/end in Whitby rather than Oshawa - they head straight to/from Whitby yard, to avoid the bottleneck at Oshawa.
The turnback platform doesn't need to be at Aurora specifically, it just needs to be somewhere they want to terminate some of the trains. Mulock or East Gwillimbury seem like good alternative sites where space is less constrained than at Aurora. In fact it doesn't even need to be a platform, it could alternatively be a tailtrack between stations, but that's less optimal for passengers since it eliminates the convenience of having the train already sitting on the platform when passengers show up.
Have you seen any indication that they are planning to install structures that would conflict with the future terminating track?
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