Looking at the documentation page for the retime function, the description of the method input argument states that it must be "specified as a character vector, string scalar, or function handle." It cannot be specified as a cell array of either character vectors or function handles or a string array, which is likely how it would need to be specified to use different methods for different data variables.
See the "Apply Multiple Methods to Timetable" example on that documentation page for a model you can use for your retime calls and how to reassemble the data into one timetable afterwards.
