From Memorie istoriche della città e chiesa di Bergamo (Bergamo, 1819), vol. VI, pp. 63-64:

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http://www.rosscaldwell.com/images/visc ... 819p64.jpg
The account of the standard, on page 64, reads: "... after, they presented a vermilion standard with yellow stripes down the length, which was hung in the Church of San Marco with gold letters which said Civitas Bergomi. [Ronchetti's remark] These two colors were used in Bergamo to indicate the two factions of the Ghibellines and Guelphs, the Yellow and the Red, the first for the Guelphs, and the second for the Ghibellines, which came to form the stemma of our city."
This doesn't make it clear what this original standard looked like - it seems it could have had more than one set of yellow and red stripes.
But the accounts always read "partito d'oro [or "di giallo"] et di rosso", or, as we would say, "party per pale or and gules", and since the rules of heraldry read dexter-sinister (shield holder's right to left, viewer's left to right), it would seems that gold or yellow has to be the dexter side, i.e. the viewer's left (I realize that these rules may not have been codified in the 15th century, most probably not in Italy in any case).
The historian Bortolo Belotti (1877-1944) alludes to this in what I can read of his now-standard history of Bergamo, Storia di Bergamo e dei Bergamaschi (1940; this edition Bolis, 1989), vol. 8, p. 262 -

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He says that Giuseppe Locatelli, in an article cited in the margin, showed that the stemma of Bergamo can be traced for about five centuries, and describes it as "partito d'oro et di rosso".
Perhaps it is possible that the painter of the Stemmario Trivulziano reversed the order of the colors (but even that remains to be seen), but it is clear that the overwhelming precedent rests with the order gold/yellow and red (L-R).