When purchased new
 

When a 1906 American Eagle was purchased new did they come with only one mag? Did they come with any other accessories like a takedown tool? Also how come I never see them advertised for sale with "original box", did they not come in boxes? Did none survive? This question could apply to any commercial Luger.

The combination of a Luger, two numbered magazines, and a loading tool was the result of the contracts that the Military agreed to with DWM in the beginning. These orders were likely shipped in bulk.

Commercial distribution took place under a variety of contracts with national distributors and their retail dealer networks in each country. They may have created their own retail packaging for shipment of individual handgun orders.

Commercial Marketing at the time was focused more on catalog presentation and retail in person interaction at stores. Some of the earlier individual handgun packaging I've seen came from Walther with the PP series in the 1930 time frame. In Sturgess' book on page 758 he pictures an early Stoeger individual Luger shipping carton that has the DWM name on it from about 1921 as well as a slightly later one from BKIW.

Some commercial Lugers were also sold in fitted cases, again not necessarily provided by DWM.

So if someone bought a new commercial Luger back in the day and wanted another mag or other accessories did they have aftermarket items that were being made? Was the only option buying factory made mags, loading tools etc. ?

Most likely the dealer that sold the Luger would obtain extra magazines and tools from the manufacturer's distributor that they already had the relationship with.

Patents encumbered the designs of most firearms for the first decades of their manufacture. If an aftermarket manufacturer were to make them, they would be paying design royalties to the patent holder.

Aftermarket commercial items were unlikely, but of course possible. Some of the countries using Lugers licensed the design and had their own magazines made locally. Think of the Swiss and Dutch Lugers. Erfurt had them made for their Lugers under license, and Haenel Schmeisser made their excellent welded and milled steel magazines, which were used for some Commercial Lugers.

The earliest non DWM / Erfurt / Mauser / Krieghoff / Simson 9mm Luger magazine I own was made after WW-II. It is bright nickle plated and made by ERMA.

the only aftermarket item you'll find is holsters - now boxes - rare as hens teeth -

you see ones like this
https://www.simpsonltd.com/products/m3486

and sometimes a Stoeger with DWM, but i Have also seen DWM boxes - I think most weren't shipped in them, or you'd see them more often. But then I have never seen a Colt SSA box?
I have seen lots of early 1920 era boxes for S&W and Colt but earlier is hard to find.