I agree with @Animosity022: I think rclone uses a single encoding for the local backend, OS-dependent but not filesystem dependent. The encoding can be configured, as indicated, see also background info about encoding in Overview of cloud storage systems. In addition: To copy from one local remote to another local remote, to be able to configure different encoding on source and destination, one would need to use connection string syntax.
You can try the following:
First, run the following to show your default encoding:
rclone help flags local-encoding
Now use the default encoding shown by that command as a starting point, and add/remove identifiers on source and/or destination to fit your need. E.g. given a default encoding of Slash,Dot, if you want to copy files from source as is but with additional encoding of colon on your destination:
rclone sync test ':local,encoding="Slash,Dot,Colon":/path/on/ntfs/partition/' --dry-run
Remove the --dry-run to actually do the sync, when you have verified it does what you want.
Edit: Added quoting to the sync command, which was necessary to make it work on linux, as discovered by @mhermann and mentioned in next post.