Does Opus Dei have greater autonomy now that it is a prelature. Can one speak of Opus Dei as a church within the Church?

No part of the Church constitutes "a church within the Church."

Personal prelature
Opus Dei - Does Opus Dei have greater autonomy now that it is a prelature. Can one speak of Opus Dei as a church within the Church?

No part of the Church constitutes "a church within the Church." Precisely the contrary is the case. Each part fosters links of communion with the whole Church. The faithful of Opus Dei are and feel themselves to be living members of the universal Church and of their respective dioceses, in whose life they take part like the other faithful. One must also take into account that this prelature, unlike what might happen in the future in others, does not carry out certain functions of ordinary pastoral care (baptisms, confirmations, marriages, funerals, etc.). Instead it dedicates special attention to the formation of its faithful and of those who take part in its apostolates (spiritual retreats and meetings, study of the sacred sciences, personal spiritual direction, etc.)

Like the autonomy that in different degrees is proper to all the faithful and to any ecclesial reality, the legitimate autonomy of Opus Dei in carrying out its mission in the Church is always an autonomy in communion with the universal Church and the Roman Pontiff and with the particular Churches and the diocesan bishops. Thus Opus Dei, in its present structure as a prelature, enjoys the autonomy proper to entities that are part of the hierarchical structure of the Church (and whose head is a subject with episcopal power), which is distinct from the autonomy proper to entities of an associative nature.