I think a stock Lotus Europa S1 or S2 is quite a rare thing to come across. At least in Germany, I have not seen many. Not even on the internet. That's why cars in completely stock condition (matching numbers) will indeed increase in value. I'm not sure, if it's possible to receive data about the matching numbers from the official Lotus archive, but if you are able to prove that your car has the original engine and gearbox (in good working order), this will be the best bet in terms of value.
Lotus Europa enthusiasts are not so much focussed on value and with it originality (compared to Porsche guys for example). A Lotus Europa from 1968 will never reach the same, not even a similar value compared to a 1968 Porsche 911. Instead, many Lotus guys favour driving fun more than original condition. That's why I think that a cross flow Renault engine is also a very good argument, which makes a Lotus Europa attractive for possible buyers, which is equivalent to value. In Germany, you can easily register a cross flow Europa S2 for the historic number plate, because it's contemporary tuning. The Swiss importer of Lotus even put this modification up for sale and named it Lotus Europa Hemi 807. But as far as I know, only in quite small numbers.
As the S1 and S2 Europas were denounced "underpowered" even by the contemporary motor press, this reputation will apply even more today. Lotus got rid of this by fitting the TC and Big Valve engines to the successor. And the owners of S1 und S2 Europas tried to improve their cars on their own. Renault cross flow engines where plug & play conversions and easy to get. But I don't think that many of these conversions received actual Gordini engines. The Gordini valve covers were also easy to get, but original Gordini engines weren't. Thus, most of them will be just ordinary R16, R17 or Fuego engines with a Gordini badge or valve cover.
Nonetheless, the Renault cross flow engine is a great conversion for the Europa S1 or S2. It's reasonably priced, light (lighter than the TC) and can also deliver reasonable power output. As jbcollier said, you can put a 125 HP engine into the car and it's not even tuned. You can also use the Renault engine for racing, if you want. In this case, a powerful engine (around 160 HP) will not be cheap, but still much cheaper than a TC with the same power. Of course, you'll not reach 190 HP as the TC, but the Renault engine had major success in the Alpine Renault A110 in the early 70s. Thus, nothing you need to be shy about.