Yes. Since Div. 1 does not explicitly state how to determine the design temperature of a component, you may use good engineering judgement and practice to do so. Applying another well known code/standard would qualify.
Now to play my role as owner/user: It sounds as though you are dealing with a case where you are close to the limit of a flange rating. If this is regarding a new vessel, just upgrade the flanges to next rating. Don't engineer in a problem for the plant engineer to deal with three years after you've forgotten about it. The design temperature of the vessel has already been determined. It is for "the vessel" including the flanges. If you somehow want a separate design temperature for the flanges, you need to seek approval from the owner/user to do so and be extremely explicit about the different DT for the flanges in your documentation, including the U1A forms and nameplate stamping. Another potential solution, not without its detractors, would be to be very explicit abuot the "spec break" between the Div. 1 components and piping: You probably have built up nozzles, i.e. a pipe neck welded to the shell and a weld neck flange welded to the pipe neck. The WN to pipe weld joint (the first circ. seam off - away from - the shell) may be chosen as the code spec break. This would allow you to deal with the DT issue for the flanges using the piping code. If you go this route, literally draw a spec break on all the fab drawings indicating that the nozzle neck is VIII-1 and the flange is B31.3. On the U-1A form list the nozzles as usual but do not include any mention of the flanges with the nozzles; in the "notes" section write a sentence stating that the scope is limited to the nozzle necks and not to the flanges.
If, on the other hand, you are dealing with an existing vessel, maybe for a rerate, you might be able to physically measure the temperature on a hot, calm day while the unit is at its normal operating temperature. Add perhaps 20 deg margin. I'd strongly advise a discussion with your AI about formally rerating the flanges to this new DT based on measurement so there will be a paper trail. Another approach would be to do a paper alteration to take the flanges out of scope as I described above.
Lots of options for you, the best depends on what stage of life the vessel is in. If practical, take the approach which makes it more robust. I never heard anyone complain that a flanged joint was not leaking. Sometimes it is not practical and then more creative approaches may be required while retaining good safety. Cost should not be an issue here as the cost of dealing with a leaking flange will be 10 to 100 times as much as an upgrade… if the leak does not cause a fire.
Let us know a bit more details about your situation, and how you choose to deal with it. Its educational for us all to know how others deal with these issues.
jt