If caltrain adopted higher platforms, they would interfere with the size of freight trains passing through.

There are ways around this: If all the high platforms were on 4-tracked sections, the freight could use the express tracks only. Mixing high and low boarding might be more painful though.

Not to mention the current train stock doesn't support level boarding, so Caltrain would be restricted to use them as express trains and only have high platforms at local stations, for example.

Or the platforms could be far away from the trains and they use extending platforms: That is potentially unreliable and costly.

There is a somewhat reasonable blog about this type of issues at http://caltrain-hsr.blogspot.com/ which is mostly reasonable though it tends to be written as if it is the only reasonable choice.