The version of the story given in the OP is clearly incorrect. Queen Victoria had a very elevated view of the prerogatives retained by her, but even she would not have ‘struck out’ parts of a bill presented to her by Parliament. The story only makes sense if it is claimed that she insisted on changes to a draft bill which had yet to be considered by Parliament.
That however raises a further problem. Those telling the story rarely specify the particular statute involved (itself a warning that this is a UL), but, if they do, it is usually the Criminal Law Amendment Act of 1885. This is understandable, as that Act contained the crucial redefinition of the laws against male homosexuality in Victorian Britain. The important point however is that the circumstances surrounding the introduction of the clause in question are well known and had nothing to do with Queen Victoria. The section concerning homosexuality was not part of the original bill, being an amendment moved by a backbench MP, Henry Labouchére, without prior announcement, which was then passed by a thin House with almost no discussion. No one, least of all the Queen, was consulted beforehand. The question of lesbianism was not mentioned by anyone.
That Labouchére’s amendment was a backbench initiative also rules out the other version of the story, which is that Victoria’s ministers were too embarassed to raise the subject of lesbianism when discussing proposed legislation with her.
What is true is that in 1921 the Lord Chancellor, Lord Birkenhead, argued against the criminalisation of lesbianism on the grounds that it would only alert innocent women to the existance of such activity.