Encrypted scripts are expected to work on all OSes. If there's a unique OS (other than windows/linux) ..i.e. openwrt, android you wish to confirm, send us an email!
Can I encrypt function files/scripts? Yes, you can. There are different ways function files can be encrypted. You can encrypt as just another script, or with additional security measures.
Is there a size limit on the type of scripts that can be encrypted? No, there is not. The size of the scripts you encrypt is irrelevant to the encryption process.
My script is very complex. Will that affect encryption? No. The complexity of your script does not matter, at all!
Will you be able to make these custom changes for us? Sure, if the customization request is deemed safe and does not introduce potential loopholes.