Tom, with respect, I do think your post over-simplifies the political and economic situation somewhat. I would have liked to have discussed a response first with Portuguese colleagues, as I’m sure they are much more knowledgeable than I. However, I would like to suggest that the (close) relationship between England and Portugal, and / or the development of under-development, did not directly result from the Methuen Treaty: important a factor as it was.
Amaral’s article admits the importance of the treaty as a constraining factor on Portuguese economic (and political) development, but asserts that it was: the continued adherence to seigneural land holding and taxation rights; the resultant lack of an entrepreneurial class / culture; the continued but declining importance of Brazilian gold (maintaining or offsetting the balance of trade deficit); and reliance upon specific imports and exports that impeded the development of an independent and thriving Portuguese domestic economy (and therefore acting as a “driver” of foreign policy).
Although Portuguese domestic and, especially, foreign policy was often in line with that of England (Britain) it was not directed by it. In the period leading up to 1799, at least four shifts in Portuguese foreign policy are visible: the first two of which were developed jointly with Spain, the third resulted from Spanish aggression and the fourth resulting from the development of the First Coalition.
Firstly, in 1778 a series of agreements and treaties between the two Iberic powers guaranteeing (mutual) security and neutrality. Secondly, during the American Revolutionary Wars or American War of Independence, a maritime and neutrality convention between Spain, Portugal and Russia. Thirdly, during the period 1789 and 1790 Spain requested the assistance of France (under an existing treaty between these two monarchies) in addressing a dispute over access to navigation rights and trade on the Pacific coast of North America. The refusal of France does not concern us here, but one outcome was the repudiation of the existing treaty between Spain and France and the resurgence of hostilities between the two Iberic powers.
Fourthly, and most importantly perhaps, is that throughout this period, and especially during the development of the First Coalition and the revolutionary wars, Portugal considered itself to be neutral. Indeed, it was one of the last countries to sign a formal agreement with England (Britain) in 1793 (26th September) against the French Republic. And its first act of aggression towards the French Republic was the provision of a military force of all arms in a joint Spanish–Portuguese army acting against a French Revolutionary army in Catalunya in 1795.