They absolutely do intend to regulate the batteries. Even if they have other uses. My best guess would be that any shop or online seller will simply remove things like the batteries, wires, silica, etc. from their offerings. Or maybe they could set up a separate company to sell only those things, but I imagine that if FDA saw that an online company selling only generic things like the batteries, wire, etc is in anyway associated (like owners of record) to a company that also sells e-liquid or mods or tanks, then it will say the intended use of the products in the generic item company is for the tobacco products in the first company, and will seize their goods for selling unapproved products.
On page 163-164:
This final deeming rule deems all tobacco products as they are defined in section 201(rr) of the FD&C Act, except accessories of newly deemed products, but including components and parts as defined in this rule. The wires, screws, and silica meet the definition of component or part, as they are an assembly of materials intended or reasonably expected to be used with or for the human consumption of a tobacco product and are not accessories of a tobacco product. FDA also remains concerned about reports of exploding batteries. Batteries that are co-packaged with other components or parts of an ENDS (e.g., cartridges and tanks) or otherwise intended or reasonably expected to be used with or for the consumption of ENDS are components or parts and subject to FDA's tobacco product authorities. However, as noted elsewhere in this document, for ENDS hardware or delivery system components or parts, such as batteries, FDA expects that it may be difficult for manufacturers to obtain premarket authorization for such products, given the great extent of possible variations in combinations of hardware components, if all considered and sold separately. Thus, with respect to such apparatus, FDA expects that manufacturers will be most successful where authorization is sought for entire delivery systems, rather than individual components. Elsewhere in this issue of the Federal Register, FDA also has made available draft guidance, which when final will represent some appropriate means of addressing the premarket authorization requirements for newly deemed ENDS products and will include FDA's current thinking regarding compliance with existing voluntary standards for ENDS batteries.
And on page 168:
(Comment 75) Some comments stated that items also used for purposes other than for tobacco use (i.e., a lighter or matches that can be used to light candles) should be classified as accessories and, therefore, not subject to FDA's chapter IX authorities. For example, batteries used in advanced personal vaporizers can be found in laptop battery packs or cordless drill packs. These comments also stated that items such as lighters and batteries may (or may not) be used in consumption of a tobacco product or are regulated by the Consumer Product Safety Act (as are child-resistant lighters) and, therefore, should not be subject to FDA's tobacco product authorities.
(Response) FDA agrees that it is not necessary to regulate batteries that are not intended or reasonably expected to be used with a tobacco product under its tobacco product authorities. However, it is important that batteries that are co-packaged with other parts of an ENDS (e.g., cartridges and tanks) or otherwise intended or reasonably expected to be used with ENDS are components subject to FDA's tobacco product authorities. FDA remains concerned about reports of exploding e-cigarette batteries and finds that regulating them can help address these problems.