The process that was followed for the Ontario Line is that a rough design was completed by the technical advisor and then improved up to around 10% for the various bids with some changes. From there the design became the responsibility of each GC for each Ontario Line package. The link you shared is regarding reaching 50% design of Civil and MEP works (basically everything to do with the Station structure itself without any of the rail-specific elements that make it a Station) at King-Bathurst and Queen-Spadina, two stations where heavy civil works began in 2023 under the Ontario Line South Civil contract. Design for the rails, systems, and vehicles is handled by a separate contract under Connect6ix for RSSOM. This design is very likely still in its infancy, with many key decisions likely in the proposal phase.
With that said, something like a subway station is easier to construct underneath a progressive design-build model (like ECLRT, HULRT, FWLRT, and the OL) because while it is complex, the construction proceeds in stages which are generally well-understood and provide milestones to aim construction towards (Roughly: Piling - Shoring - Excavation - Foundations - Interior Works - MEP - Superstructure). Additionally, with the exception of timing for TBM arrivals, individual stations on a line can almost function as individual projects valued at hundreds of millions of dollars within the larger linear project. The most important distinction is that once you get to the point of designing and constructing the individual station, the majority of the big, multi-stakeholder, process-chained decisions have been made - The land is acquired, the alignment is finalised, and construction can progress. While this is by no means an easy point to reach with something like the Ontario Line, it is worse within a project like Alto or GO expansion is working both on a much larger linear scale, and in a more clouded decision space.
A progressive model like design-build introduces many problems which scale to the remaining unfinalised decision space - in a situation like King-Bathurst Station, the decisions are made, permits are acquired, and design has sufficient lead time that construction is progressing well. In a situation like California High Speed Rail, wherein the land was not yet all acquired, the stakeholders not satisfied, and the EA not completed, the design and construction could not help but to continue to run into delays which reverberated out from the issues further back along the critical path. This is why it is crucial to understand what the Alto contract is doing, because if they are successful in clearing all of the stakeholder, environmental, and permitting hurdles, then the construction and design can proceed in a far smoother manner than Canadian Rapid Transit Construction is accustomed to. Time and money spent on these factors now directly leads to a smoother design and construction process, and If they can clear these hurdles while also generating a 50-90% design, then this would be one of the best investments in transit a Canadian Government has ever made.