Does it bother anyone else how just about every rapid transit line in Toronto uses a different form of rolling stock?
No.
30 years from now how is the TTC or Metrolinx suppose to "cost effectively" procure trains in the future if every line is designed to use different trains? Instead of one large procurement that'll cover all the lines, they now have to do a bunch of individual procurements for each line separately.
You don't. This is a luxury open only to "new" systems which were standardized in the very recent past. The world is filled with "legacy" systems that inherited a variety of different rolling stock and infrastructure built to various different specifications, and is really not a big deal. Doing one large procurement also seems unwise, so we should be thankful for the fact that we will be unable to:
a) if the vehicle turns out to be a lemon, now your ENTIRE network has to contend with that problem
b) because different vehicles were built at different times, trying to do a wholesale replacement would result either in vehicles being prematurely retired because we have new ones now, which is a waste of money, or in vehicles having their lives artificially extended, possibly beyond the point of feasibility, because you don't want to waste money by retiring something on another line that is only 2/3rds through its lifespan. For example: the TRs will be life expired in 20 years, the T1 replacements will come online in, say, 10 - how would you possibly replace both at the same time? Or the legacy Flexitys, despite being ostensibly similar to the Line 5 Flexitys, the oldest cars are already 1/3rd of the way into their natural lifespan, while the Line 5 Flexitys, despite already being 3-4 years old, have yet to carry a single revenue passenger. There is no way you could coordinate this, either.
Not just with the metros ( T1, Toronto rocket, Hitachi), but with the LRT's as well. Is it true that the Eglinton line and the Finch west LRT use different LRT trains?
They will, but both lines are designed to use off the shelf cars as much as possible. Both run on standard gauge at 750 V, so any vehicle that fits these specifications should be able to physically run on the line. They use different signalling, Line 5 uses Bombardier's Cityflo CBTC system, while Finch West uses Thales Seltrac, which may pose a slight difficulty, but then, I see no point in a primarily overground LRT line using anything but line of sight operation.
What's the likelihood that at some point Line 1 & 4 will be standardised with the Ontario line?
Zero chance. It would be a massive investment that would bring no tangible benefits to anybody - if anything, it would end up crippling line 1 because now you'd be running smaller trains with less capacity. Any automated replacement for the TRs will be built to the same body dimensions, which means you'll be benefiting more than if you ran the Hitachi gadgetbahn on it.
The real question we should be asking ourselves is why Metrolinx is using 'light' metros and leaving capacity on the table for the most important transit project of our times, instead of the traditional RT-75 style rolling stock that we are well used to in Toronto. I suspect you won't be getting that answer, and even if you did, you would find it unsatisfying.
I just feel that the more coverage a transit agency can achieve with fewer types of rolling stock, the more efficient the whole operation can run.
That's a nice theory, but it doesn't seem to hold back the Europeans, who run much more efficient operations, as a general rule, with larger varieties of rolling stock than we do here. And again, the concern about being being locked in when you've purchased a lemon comes to mind.