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The short answer is yes, these modern ores would generally have been discarded as waste rock or slag. To understand why many modern ores would have been discarded at a given place and time, it is helpful to ask these three questions: 1) Does this material exist here? 2) Is the target ore mineral valuable in this era? 3) Does the target ore mineral exist at a sufficient grade (%) to allow economic extraction with the current technologies? Let's look at these questions in greater depth.
Economic ore deposits of any given kind only form under specific geological circumstances, which in turn means that their global distribution can be highly irregular. As an example, bauxite ores are laterite deposits that form almost exclusively in warm, humid regions (i.e., not Europe). Likewise, platinum and palladium are PGE elements, which are extremely rare in the crust due to their high masses and chemical properties; the Bushveld Complex of South Africa alone holds more than 75% of the world's reserves (Ridley, Ore Deposit Geology)! Hence, none of the ores you mentioned would even be present in economic quantities in Europe or many other significant historic mining centers! One interesting historical consequence of ore deposit distribution is the absence of a "bronze age" in much of North America; bronze is an alloy of copper and tin, but the only known tin deposit on the continent that had a high enough grade for ancient mining was in Mexico. As a result, bronze played little role in civilizations like the Mississippian culture.
As you noted, many metals and minerals were only recognized in the early modern era. If the target mineral had no value at the time, it naturally would not have been mined, or would have been treated as gangue if it were mined with something more valuable. It should be noted, however, that some materials valuable today were valuable historically for different reasons; a good example of this is aluminum, which is today mined primarily from bauxite ores but was mined in Europe historically as alum for use in dyeing fabrics ( Agricola, De Re Metallica http://www.gutenberg.org/files/38015/38015-h/38015-h.htm#Notes_569 ). Aluminum metal would not be used in any meaningful sense until the 1880s, when electrolysis made it feasible to smelt. Between 1824 and the 1880s, the metal was so rare that there was no economic demand, which ironically made it uneconomic to mine on an industrial scale.
The cutoff grade for mining any material depends directly on the technology available to the miner. Considering that the ancients had access only to relatively primitive smelting techniques, they exclusively mined high grade ores. If Ötzi or some other ancient prospector had stumbled upon the 200 million tonne Bor copper deposit in Serbia, he would have walked right on by because a Cu grade of under 2% would not only have been of no value, it would not even have been noticeable! A fun result of this is that one man's waste might be his distant descendant's gold mine. Strabo, writing around 30 B.C., stated that "the silver mines in Attica were at first of importance, but are now exhausted. The workmen... committed to the furnace the old refuse and scoria, and hence obtained very pure silver, for the former workmen had carried on the process in the furnace unskillfully" (from Herbert Hoover's commentary in De Re Metallica). Even today, many mines derive significant revenue from reprocessing 19th century mine dumps with modern methods.
So, considering these questions, if a modern ore mineral were a valueless gangue mineral at a given time and place, what would the ancient miners do with it? If it were in the wall rock of the vein, they might have separated it out and piled it in a dump; otherwise, they would have smelted the ore chunks and separated the gangue as slag. Not so dissimilar from how it's done today.