Roland...you are correct on everything you said. I'm not gonna disagree with you. Yes, I am assuming representation...so each scientist is good for six beakers. But in order for the cottage/town to be better, you are assuming a no-less-than 90% science rate. At 80% (80% of 7 commerce is 5.6 beakers), the science specialist becomes a stronger researcher (with representation, anyway). And specialists and cottages/towns are not entirely mutually exclusive. A coastal city with seafood resources and another food resource can support several scientists, and you can still have some cottages/towns in the city radius.
The original topic was on combining the great person farm with science city...and I am making the argument that such a strategy can be very good. It leverages your specialists in two ways, instead of just one (solely for great person points). Identify your GP farm first. Lots of specialists, and the National Epic. Now take it the next step. As long as you are setting a bunch of specialists for your GP Farm, make those specialists scientists, and add Oxford, an Academy, and the science improvements*. You now have a GPF and a Science City that uses the science specialists for two purposes, enhanced by your national wonders. And this science city is not as dependent on your science slider. You can drop your science rate for a while, and with a science city developed this way, you can still research at a high rate. The downside is that you do lose flexibility in great person points...you want to keep your specialists as scientists under this strategy. But I would argue that there is nothing wrong with constantly getting Great Scientists.
The question gets to be a tradeoff...you do indeed give up an extra commerce by going with specialists instead of more cottages/towns, but in exchange you can gain the great person points. And by popping Great Scientists at a high rate, you can use them to make up for that lost commerce/science over time by joining them up as super-specialists or directly researching techs.
*An alternative would be to make the specialists merchants, and add Wall Street (instead of Oxford) and the money improvements (market, grocer, bank)...this can be particularly good if you can get this in a city with a lucrative shrine. This will generate good gold, even while running a high science rate.