This is all true. However, on this web site, I often refer to the older place names, even though these places don't exist anymore. First of all, many of these places are still on maps.
People still use the place names.
Secondly, historic documents are filed according to the boundaries that existed at the time. If you are looking for census records for Scarborough, you look under Scarborough, and it doesn't matter that it no longer exists. It would be just too confusing for people who don't know the area if I started changing everything to reflect what the Ontario government has recently done to our borders. They don't change the fact that your ancestor lived in York County - he did not live in the York Region, because the York Region did not exist until 1972. I hope that this makes sense.