Your solution in post-processing the QGIS output pdf is probably your best quick'n'dirty solution.
QGIS carefully keeps track whether label font sizes, line widths, etc., are specified in map units or in image units (mm, points, etc.). So your e.g. 1mm line which looks great in 6x9 will be too small if looked at from a reasonable viewing distance for 24x36.
It is somewhat painstaking, but where I have built maps which I knew were going to be outputted in different "form factors" and read by users from different visual distances, I have used expressions with variables to help.
Define a variable
symb_scale with value
Project / Project properties / Variables.
In your layer symbology (and labeling formating), wherever you specify a fixed size, e.g. 0.66 (mm thick line) or 10 (pt font), instead do a data-defined over-ride with expression
0.66*@symb_scale (etc.) Make the sizes look good on the map canvas and/or your default layout.
In additional, special layouts, like your large poster, over-ride the scaling by redefining
symb_scale as a layout variable with a different scaling factor, say
'3'. You do this under
Layout / Properties with the variable panel being way down at the bottom of the right-hand panel. The expressions in 2. will now mean that within this layout, all lines / fonts will be 3x as large. You can set the factor differently for different layouts. For instance, a poster map (to be read at large distance), a 11x17 map (to be read close up, with lots of detail), and an offline MBTiles map loaded onto pocket devices with a wacky scaling factor.