I realize that this thread is more than a year and a half old, but I hope that my response works for some newer users.
Use your main file or files in the usual way. Fortunately, for me, my projects can generally correspond to the one project, one file rule. That file has a selected border size that is set at a 1:1 scale in the print settings.
My default drawings have almost all of the layers preset and in order so that for single story or two story residential or commercial, I just open the new file and go. Once in awhile, I'll have some uncommon condition that necessitates extra layers or new layers, but that isn't a big problem.
If i assume that I will be printing a two story residence on 24x36 sheets, I use my 24x36-2R default drawing.
My first layer in the file list is named 24x36. It has the border lines, project title, misc. disclaimers, etc., all of the things that will be common to every drawing sheet in the final set.
After the border comes layers for plans, elevations, sections, details, schedules, and so on.
Following the actual "drawings" are layers for the sheet numbers and sheet names. Cover Text, C1, C2, C3. S1, S2, S3, A1... A20, M1... M4, E1... E5, P1... P4. Those entities are all overlaid as needed for their correct position on the border.
The next group of layers is what makes everything work for me. Their names are C1XRefs... C3XRefs, S1XRefs... S3XRefs, A1XRefs... A20XRefs, M1XRefs... M4XRefs, E1XRefs... E5XRefs, P1XREFS... P4XRefs. All of the sheets are created as GoToViews with the sheet numbers as the GoToView name. Each print sheet will have only three layers that are on, the border, the sheet number/name text and the corresponding (sheet number) XRefs.
By doing this, I can modify drawings more easily than I could when I used multi-layout for plotting. I really liked multi-layout, but this just seemed slightly better for me.
Which now brings us to the original question of document sets with different size borders.
I would simply create a secondary file for the odd size sheets set using my 11x17 default drawing. I'd build the sheets by inserting the XRefs of the original drawing file as needed and at whatever scale worked best. Most would be almost always be at half the scale used for the 24x36 set. That's why I have gone to graphic scales for almost all of my work. I also have slightly different pen settings for smaller scale drawing sets to keep text readable. This system also makes a single print layout work for all of the drawings in the set.