There is always the Rhino Eco-Coat option. Expensive, but will put the argument of caulk versus Eternabond to rest for good.
If I were planning on selling my rig, I'd use caulk because that is what buyers expect.
If I were going to keep it until the wheels fell off, I'd use Eternabond and EternaCaulk on the edges of the tape so dirt doesn't lodge there and cause it to look bad. One can get Eternabond in varying widths up to 48" by 50 foot rolls, so done right, it can be used for a good seal. It looks ugly, but Eternabond does solve the problem and does the job for the long haul.
Of course, before any re-sealing, I'd make sure to do any replacements of roof stuff, from a new RV skylight (might as well replace it and coat the replacement with 303 Aerospace Protectant so it will last a bit longer to the UV rays), to better vents for the black/grey tanks (either the passive ones that use a venturi effect with the wind, or one that uses solar with a small fan), to updating the vent with a Fantastic Fan.