Jonny’s primary guitar is a Fender Telecaster Plus V1 which was purchased in October 1995, after the band’s gear was stolen in Denver on Oct 03.

Jonny playing his Tele1 at Coachella, 2017.04.14.
While you are correct that most Fender Telecaster Plus V1 guitars (those produced 1989-1994) have the serial number on front of the headstock, the Telecaster Plus’s headstock was redesigned in 1995 along with the rest of the Fender range for the company’s fiftieth anniversary year. Telecaster Plus V1′s produced in 1995 have their serial number on the back of the headstock. Fender redesigned the Telecaster Plus in 1995, changing the pickup configuration, but V1 Plus guitars were shipped out throughout that year. It’s likely that Fender produced the V1 until they had used up all of the parts specific to the guitar. If you check ebay or reverb, you can find several Tele Plus V1 guitars from 1995 which feature the 1995 headstock design.
Jonny’s current Telecaster Plus No.1 is from 1995, purchased right after the gear theft. You can’t see the fiftieth anniversary decal on the back of Jonny’s headstock due to the small menorah sticker which he placed over it.

Jonny playing his Tele1 during the The Numbers music video. One can lightly make out the quotes around the word “Telecaster” on the face of the headstock, which were introduced to all Fender Telecasters in 1995.
Additionally, the Tobacco Burst finish of Jonny’s Telecaster Plus was never offered for American Standard Telecasters. The most similar finishes offered for American Standard Telecasters were “Brown Sunburst” and “Sunburst”. An example of a American Standard Telecaster in a “Brown Sunburst” finish is Jonny’s Tele2, which was converted to Tele Plus specs.

Jonny playing his Tele2.