This issue has been added to the tracker:
Issue 1768 – Allow other 2xx responses to PWD command, not only the standard 257
You can vote for it there.

Will see if other users face this issue as well.

So, maybe do just some option for this case and do not drop connection after received response code 250 and send
CWD / command as do other FTP clients?

The only allowed positive response code to PWD command is 257. Your server violates the specification by using a code 250.

PWD
250 "/" is the current directory.

See RFC 959:

Essentially because the PWD command returns the same type of
information as the successful MKD command, the successful PWD
command uses the 257 reply code as well.

Try to login a specific FTP-server. WinSCP cannot obtain current remote directory from
remote FTP-server. The log file attached to this message.