I think that your first interpretation (implying Kyoto/Kamakura goods are obviously from there and do not need explanation) is the meaning here. So, I've used "of course" for もとより.

A possible translation of the beginning of your sentence could go something like this:
Consequently, there were, of course, goods from Kyoto and Kamakura, but via Western Japan, products came in from Korea and China…..


もとより has the meaning of 初めから (from the beginning) but it also has the meaning of もちろん(勿論) which is "of course." (Shogakukan J-E Dictionary)

勿論 is defined in the Nelson’s Japanese Character Dictionary as: naturally, of course (in this order).

Also, そのため can be translated as “consequently.” (Shogakukan J-E Dictionary)

I hope the following is the author's point:
Andou clan had as many as five trade routes: The first one is with Kyoto, the second one is with Kamakura, the third and fourth one is with northern areas (カムチャツカ、樺太), and the last one is with Korea/China(大陸). Consequently, not only the items from Kyoto/Kamakura (implying it is obvious/ needless to say so because they are domestics) but also items from Korea/China went into Tsugaru via western Japan, their base, and so does ones from northern areas via northern route.

Although this translation cannot be found in any dictionaries, I guess it would suit best in this context.

Meaning of the word is already explained by other answerers. But in this case it (もとより) is used as emphasis.

To answer your following question directly:

Does もとより here act to separate 「京都、鎌倉の物資」with 「朝鮮や中国の製品」(implying Kyoto/Kamakura goods are obviously from there and do not need explanation), or does it connect 「京都、鎌倉の物資」with 「朝鮮や中国の製品」saying that the origin of Kyoto/Kamakura goods are Korea/China via western Japan?はもとより、西日本を経由して朝鮮や中国の製品が入り北回りのルートからは毛皮、海産物、鹿の綱などの北方の物産が集積した。

Your latter guess is closer to be correct, but not quite.
Roughly speaking what it says is ........
The Tsugaru Peninsula, the area ruled by Lord Andou is a trade center due to its geographic advantage to these five different trade routs. There trade goods from even China and Korea via Western Japan were amassed (or whatever word you prefer). This included, needless to say, goods from Kyoto and Kamakura areas.

Therefore, goods from China and Korea are not necessarily imported via Kyoto and Kamakura. Rather, they came to the Peninsula directly via these routs (cited in first part of your quote).

The literal meaning of もとより is "from the beginning/base/foundation" so you could translate it as "To start with..."
However, it's main purpose is to show that the first item(s) is "a given" or "of course" or "as a matter of course".
I usually turn this around in English to emphasize the first item(s) and to show that the latter item(s) are less of a given, use the connector "as well as" for the latter. I hope this makes sense.

もとより［固より｜元より］
（初めから）from the beginning; （元来）originally; （勿論）of course
E-DIC、朝日出版社

http://bulo.hjenglish.com/question/17003/