Thanks for your suggestion. Will see if more users ask for this.

Meanwhile, you can synchronize the timestamps (remote to local) after the upload:
https://winscp.net/eng/docs/ui_synchronize

UI:
Checkbox at "Transfer Settings" > "Upload Options".

Behaviour:
After a file is uploaded to a FTP site, WinSCP should recieve the actual timestamp from the server and set it in the local file (changed date).

Background:
There are some FTP servers which don't support setting the timestamp remotely. They will use their actual local time as changed date.
So you'll get different timestamps for equal files - which will become a problem when synchronizing.
When you fetch the timestamp from the server and write it back to the local file they'll be equal.