The question comes into play lately as newer command options in compare have been introduced that mimic the SharePlex parameters for those commands. For example, compare has threads and parallelism command options and the corresponding compare parameters SP_DEQ_THREADS and SP_DEQ_PARALLELISM have existed since long.
The idea behind introducing command option is, if users want to run the command on the fly using a particular value as a command option but want to retain a default value for that option by way of the parameter for other issuance of this command, they can use command option on the fly and the parameter setting as the optimum (or default) value in lieu of using command option. This is a design change and is implemented in compare/repair commands. As a general rule, if the options to a command can be put in at command level via sp_ctrl or via SharePlex parameter, the one set at command option level takes precedence over the one set at parameter level in case of conflicts.
