Interesting thread
Let me start by making a small correction to eteb3’s use of the term “quasi partnership”. What he describes would not make a company a QP. A QP is how a court might characterise a limited company whose main shareholders have a personal relationship of trust between them and an underlying understanding, not perhaps in writing, to work and make decisions together. You can’t create a QP by using such terms. It exists or not according to, ultimately whether a court might interpret it as such.
But you are correct that contract based agreements between the shareholders might open up options for enforcement ,For example, when two people set up a company say 60/40 in circumstances that make it possible for a court to classify it as a QP (agreed to always work together in running the company) then if the 60% votes the 40% off the Board , the latter may have a good case that, whilst he cannot avoid being removed as a director, he has potentially a breach of contract claim or indeed grounds to argue ‘unfair prejudice’ under s994 CA 2006.
Turning to the direct issue of alphabet shares, yes a Shareholders Agreement could well create contractual rights over the threshold for removal of a director that, whilst not preventing action being taken in accordance with the Articles /Companies Act , create options to claim compensation for loss/damage caused by the breach (failure to honour higher voting level.)
As to “beneficial ownership”.its not exactly as Clinton describes it but is the right to enjoy the benefits and rights in law (as opposed to rights agreed under contract) connected to the ownership of the shares). This will generally not be a concern to most people since it applies only to those who has acquired shares in limited circumstances under which some other person may have the right to beneficial interest, eg when shares are put in the name of X but with X acting on behalf of Y, who paid the price and is the real owner. Similarly you may not be the beneficial owner if some condition precedent to your acquiring the shares has not yet been satisfied, eg payment. So A can agree to sell shares to B but beneficial ownership does not pass until payment has been made.