In my personal opinion, there is little value to upgrading to PE. The true value is when you use your miles to upgrade to Upper Class.
You're right that you have to buy a more expensive economy ticket (around 1k for Japan usually) but remember you do earn full miles for these tickets (for the class your paid for).
So for example:
Econ LHR - NRT = c6k each way or 12k return
Upgrade cost = 40k miles
Thus net cost of 28k miles (less if you earn miles by using your VS credit card)
If you are gold for example, you get 100% bonus which means it would be 24k return earned meaning a net cost of just 16k miles.
In any event, c GBP1k plus 28k miles is pretty good value for money for Upper Class.
Best regards
Jon
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