Downside?
Other than cost and a little more weight, I am not sure what the downside to undercoating your car might be. Just make sure that there is minimal overspray.
When we lived in Louisiana back in the 80s, I saw a lot of fairly new cars showing signs of serious rust. We bought a new Jeep Cherokee in 1985, and I wanted it to last. I took it to a place that performed rust-proofing - called Ziebart. I believe they have a series of locations in different parts of the country. They would drill holes into closed sections in inconspicuous places so they could apply their special formula of coating into places otherwise hard to get. Then they covered the hole with a plastic plug (with their hallmark embossed, so you knew your car was Ziebarted). When we got rid of the Jeep around 20 years later, there was no sign of body or frame rust, even though the Jeep went its first 5 years in Louisiana heat and humidity, most of the time out of any garage. By the way, there was so little really cold weather in southern Louisiana that salt applied on the roads was not an issue.
Should you decide to drill any holes to help with applying the coating, please be sure to drill only in areas where stresses are minimal (i.e., in the sides of beams and NOT in the bottom or top). If in doubt, do not drill.
Good luck with finishing your car!