Institutions are not neutral in their effect. They operate on the basis of processes and rules. What those rules are can affect outcomes. Had the Labour Party adopted the same rules for electing the leader as the Conservative Party, Jeremy Corbyn would likely never have become party leader. Under the Conservative rules, MPs reduce the number of candidates to two (assuming more than two are nominated) and those two names are put to the party membership. Jeremy Corbyn is not likely to have been in the top two selected by Labour MPs.
The rules for electing the Conservative leader are about to be employed. There is much talk of Boris Johnson as the successor to David Cameron as party leader. However popular he may be among party members, he has first to make it to the last two selected by MPs. There are other potential candidates who have been busy building a parliamentary base. Johnson may have built up support in recent months, but he did not appear to have much of a following last year. There is talk of an ABJ (Anyone but Johnson) movement, which may mobilise behind a particular candidate. It is always possible he may suffer the fate of Michael Portillo, just being squeezed out from being in the last two. I am not saying that will happen, but rather emphasising the importance of the rules.
The same applies in the context of the EU referendum. Parliament legislated for it and stipulated the question. (I have previously commented on the significance of the wording.) However, there were no rules laid down as to a threshold for turnout or what proportion of the electorate needed to vote for the result to take effect. One could argue that formally no such rules were necessary, given that the referendum was advisory. However, without any such qualifications, it is not politically feasible to act other than in accordance with how a simple majority voted. Had there been a requirement, say, that a two-thirds majority was required for a major constitutional change (not unusual with some organisations) or that all parts of the United Kingdom had to vote to withdraw from membership of the EU, then the outcome would have been different.