A very true statement. Unfortunately FJ died in period because of the costs associated with this non-standard engines (and other components) and today we seem to be reaching the same point with cars built to the intent of the original formula being completely outclassed by cars with engines that produce power that has no resemblance to that produced in period by correct engines. Improvements in technology would give some gains but not to the extent you have mentioned with the BMC engines- or with Ford engines a 30% increase.
But the non-standard components they were talking about were things like steel cranks and rods, the majority of original Ford Junior engines ran quite happily with a Ford road car crankshaft (albeit specially prepared) and reprofiled camshafts etc.
They weren't talking about blocks & heads, which would have been illegal anyway, it was a pretty cheap formula and the cost of a steel crank/rods would have had a significant effect on the overall cost at the time.
The real problem with the cost was the presence of all the works (or semi-works) teams, who had the best of everything and pushed the costs beyond the reach of the amateurs who originally made the formula.
That is one reason they replaced it with two formulae - F2 for the wealthy & F3 for the less so, being the intention....
If you think that current FJ costs are escalating you should look back 20 odd years to the introduction of Richardson engines - my Lotus 22 was worth around 12 grand and had a £2,500 period correct engine and then someone came along with a 10 grand engine that was so much quicker you hadn't a hope in hell of competing. I don't think anyone is doubling the already substantial current prices of Juniors as happened back in the good ole days...
Given that the engine in question had a non-Ford head and was oversized (using DFV pistons - that 'oversight' was later corrected) it clearly didn't meet the original regulations and that was the time to do something about it.
Nowadays the FIA rulebook says that Richardson heads are acceptable since they are interchangeable with the original - I assume the word interchangeable lost something in translation since the inlet manifolds don't transpose...