how will the SEs know we carry the specific items?
In general, the SE won't know anything that's not contained in the product description.
However, I think your concern about the lack of specific landing pages for each variant might actually be beneficial to customers. Who wants to wade thru 65,000 product pages to find a 10mm Chrome Widget?
Your product taxonomy should really not exceed 20 top-level categories, or about 100 categories in total. Within each category, any items "below the fold" get lost, so I try to limit a category to 100 items. That equates to about 10k products per "store".
Right now, with 65k landing pages, you have too many opportunities for a customer to "get lost". By combining variants into a single landing page, you're making it easier for the customer to find that "Chrome Widget", then it's easy to see the 10mm variant among other variants.
With less landing pages, you also concentrate inbound links onto fewer pages, which should help your ranking over time.
If you also sell on eBay, you could have a problem with multiple variants, as eBay forces multiple variants to have the same shipping weight. eBay also displays the cost of the lowest-cost variant (not the first variant) which could be problematic.