You can use the Apple Mail - Rescue Good Messages script to work around a problematic server junk filter. Whenever the script runs, it will tell SpamSieve to examine the messages in the Junk mailbox, leaving the spam messages in place but moving any messages caught by the server filter that SpamSieve thinks are good to the inbox. In order for this to work, you should follow the instructions in the Setting the Junk Mailbox in Apple Mail section of the manual to make sure that SpamSieve and the server filters are both using the special Junk mailbox.
You can change the pMoveBlueMessagesToTrash setting at the top of the script from false to true if you want it to move blocklisted spam messages from Junk to Trash, i.e. to match the Move it to the Trash if the spam score is at least setting.