Perhaps you are unaware, but the Eglinton Crosstown, Sheppard and Finch LRTs are not being built by the TTC but by Metrolinx. The TTC has nothing to do with them at all. They will simply be running the operations of them in terms of ticket booth, operators, drivers etc. The trains, infrastructure and construction is all owned by Metrolinx.
Same would go for Smarttrack/GO RER. It would be built/funded etc by Metrolinx, and would probably be run by GO transit with some sort of partnership with the TTC to allow crossover Presto use by someone who is travelling on the TTC.
Remember, by the time Smarttrack/GO RER is complete, there will no longer be "TTC metropasses, TTC tokens" etc. It will all be PRESTO.
All that will happen is if you paid for a TTC fare already (were already on a subway etc) you would tap your PRESTO card and not be billed for taking Smarttrack/GO RER. It would be considered a free transfer.
Same if you started on Smarttrack/GO RER and transfered to TTC.
If you took the GO system beyond the limit of Smarttrack (transfered to a GO train and kept going to say... Brampton) when you got off the GO train you would tap your PRESTO and be billed for the change in zones.
TransitPolicyChanger already substantially covered the point that I was going to make. But yes, the key difference between the projects that you mention (Eglinton, Sheppard, and Finch LRTs) and SmartTrack is that the former do not share any trackage with any other services. Metrolinx would be operating it in relative isolation.
SmartTrack trains, on the other hand, would need to be slotted in between GO RER trains on incredibly busy rail corridors. Georgetown South especially, which will be seeing trains every couple of minutes or less during peak periods. That kind of coordination would be very difficult to pull off with 2 agencies operating frequencies like that on the same corridor, using the same station infrastructure. It would be far easier for Metrolinx/GO to own and operate both services, and be able to scale the frequencies and work out the schedules in a holistic way. It also allows both services to use the same rolling stock and maintenance facilities.