EVERYONE does this at some point.
I did it with engines a few games ago.
My common one is troop transports with no cargo handling.
I picture my valiant Space Marines storming the beaches of Normandy-4....one soldier every five minutes. >_<
Yards can only construct/refit ship classes that are lighter than the ones they were originally tooled for.
Not true. For building at a yard, what matters is that the refit cost from the tooled design to the new design is under 20% of the build cost of the tooled design. As there is a penalty to the refit cost if there is a chage in size (either up or down) large changes in size will usualy put it out of the range of available designs.
Refiting on the other hand can be done from any ship to any of the designs that can be built at a yard. However it can become prohibitivly expensive to do so, particularly across large changes in size.
I think his original point is valid though. If I design a 30,000-ton cruiser, build it at a 30,000-ton rated yard, then make minor modifications (say, electronics) that bump it up to 30,100 tons -- I can't refit at that yard without increasing it to at leat 30,100.
But as long as the refitted design is within the yard rating, then yes...it can refit heavier without retooling.
In general, making changes to electronics/avionics can be done without retooling. Changing out engines or a newer jumpdrive typically requires a retool. Weapons vary, depending on how large and how much of the ship is guns. I find that I can often make a "base" FAC, then design variants (laser, MW, meson, etc.) that can be built all from the same yard.