Hi vanity - the Remember Layout feature is for causing the particular routine you're looking at to reopen at its current window size, column organization, etc. You have to save the routine to disk and reopen to make it work.
However, to answer your question no there isn't currently a way to automatically reopen routines with FlexTime alone. This is something that is on feature request list, and in the mean time some people have worked around it by automating the process of opening FlexTime with an AppleScript that opens all the routines they care about.