Theoretically, the lined carbon steel pipeline does not require corrosion allowance to the minimum calculated wall thickness required for the pressure containment. Also, the piping comes in schedules, not minimum allowable thickness. That is, the rest of the thickness is for mechanical strenght and corrosion allowance. Assuming that the external corrosion has been excluded by your external PE protection and cathodic protection, there is no reason for the pipe not lasting 1000 years, let alone 50 years.
Personally, I am sceptical of the above assessment and I prefer engineering judgement. In reality, the internal and external linig and cathodic protection will only minimize the corrosion and the piping break down.
I would start estimating a corrosion rate for the un-lined pipe, calculate for 50 years and add some percentage for unknown conditions. Add this to the pipe minimum thickness as corrosion allowwance, select the next up pipe schedule. Then provide the best corrosion protection (internal/external) for your pipe and work out some thickness monitoring system for the next 10 - 15 years, in order to have an idea of how the system works and maintains it's integrity.
However, as you mentioned, 3 mm corrosion allowance is a symbolic inclusion, rather than engineering calculation, hence no real value, unles confirmed by corrosion rate estimates as per above.
cheers,
gr2vessels