The lithium ion 12V battery costs 3X what the current maintenance free lead acid battery costs. In the Model S, Model X replacing the 12V battery requires removing the front trunk bin and under hood trim. Tesla designed the Model 3, Model Y so that accessing, replacing the 12V battery is much easier requires less time to perform this service. On the other hand the latest Biodefense mode feature on the Model 3, Model Y means that the larger air intake housing has to be removed to access the 12V battery.
Other than for auto racing where the lower weight is a benefit a lithium battery may not be the best choice for an automotive 12V battery. Lithium batteries do not perform well in cold temperatures or tolerate high temperatures without active cooling. Manufacturers of after market lithium ion batteries such as Ohmmu claim that the lithium battery will last longer than a lead-acid battery but where is the data to back up these claims?
Another option would be to use an absorbent glass mat (AGM) 12V battery. That is what Toyota uses in the Prius and what GM used in the Chevy Volt plug-in hybrid and now in the Chevy Bolt EV. An AGM battery is maintenance free, can be installed in any orientation and can be placed inside the passenger compartment, i.e. below the floor of the cargo area. AGM batteries do cost about 2X as much as a conventional flooded lead acid battery. There doesn't appear to be a deep cycle AGM battery of the needed size, dimensions to fit the Model 3, Model Y that has the 45Ah capacity spec'd by Tesla for the current 12V maintenance free flooded lead acid battery.