Oh my, "flags"--a can of worms.
You've identified one hiccup, star count. The 48 star flags was used until 4JUL59. There was a 49 star flag used from 4JUL59 to 4JUL60. The 50 star flag has been used since that last date.
Then, there's an issue of size. USN scales its flags by size, from #1 to #7.
Here's a link: https://www.history.navy.mil/research/library/online-reading-room/title-list-alphabetically/f/flag-sizes.html --this size used is related to the size of the ship, and whether a holiday or special occurance; since 1995, combatants have a very large (1,2, or 3) Ensign as a "Battle" (and "Pride") Flag:
So, the size of the flags are scaled to the ship's size. This includes the signal flags as well.
Isn't all this fun?
Now, while dry transfer can help, there are other solutions. You can get water-slide flags from a number of sources, if not always as documented as might be desired (and, ok, at 1/350, the difference between a #1 and a #2 is ±1/32").
My go-to for flags is a product I use for cooking--heavy duty aluminun foil. Not the stuff at the grocery store, but the restaurant supply store variety (you can feel the difference).
A 300 yard roll will last you a good stretch (unless you cook a lot of briskets, or steam-baste fishe, etc.) The HDF makes really great tarps, straps, rifle slings, etc., too.
I cut a strip th width of the length of the flag to be used. Then I gin up a jig of whatever is handy in a "U" sort of shape, The foil is bulldog clipped to the ends of the jig. The thread for the hoist is held taut at the top with blutac, and it all goes in the bench vise held up vertical. (You can also just use the edge of your bench and somehing nice and flat, but, you wind up with more gymnastics.)
Get the decal into water and ready to place. Slide it over the thread and foil at the fold point, you want it to "stick" to the foil on both sides (this is where using the bench is weird, you need to stick one side, then lift the thing up and get it stuck to the other side of the foil before it dries or gets less-sticky).
When you get the drap right, it's a good idea to snug the hoit thread up into the decal.
I use plenty of setting solution for this, but solvent very sparingly. When this all dries, bend in the ripples very carefully. When happy, then use plenty of decal solvent to make sure it all sticks nice and hard. Set this off in a corner of the shop where it will not be disturbed and let it set up a couple of days.
Maice part about this method is that you can now handle the fragile thing by the tread, and not by having to touch the flag that musch at all.