I only quickly read the OP, so forgive me if it doesn't help you, but I have always been lead to believe by my accountant that airmiles are one of the few benefits left untouched by the inland revenue, therefore you should enjoy them as a perk for your personal travel plans.
I too am a director of a limited company, and the amount of tax we pay is extortionate to say the least once you go over the dividend allowance.
For this reason we prefer to buy J flights (normally discounted non-flexible, though) rather than buy WT+ and MFU as at least the cost of the flights is going against the profit of the business. Miles can then be used to buy flights for leisure travel, non-taxed.
When the prices rise to high levels, e.g. just a few days or weeks before travel, then I MFU WT+ flights as it makes financial sense.