Explain to your son that the Pope has allowed bishops to permit female altar servers. If an individual bishop permits female altar servers in his diocese, a priest can permit them to serve at the Mass. Apparently this is the case in your diocese: With permission from the bishop, some priests in the diocese allow female altar servers and others do not. It is an issue on which the Pope has allowed local dioceses the freedom to choose to allow female altar servers.
To make this more understandable to your son, you might make this analogy: As his parent, you can decide to allow him and his siblings the freedom to make decisions within certain specified limits. So long as they remain within those limits, the children may make different decisions according to their individual preference. In the same way, on this issue the Pope has allowed local bishops the freedom to adopt different policies. If a bishop decides to allow female altar servers, he in turn allows his priests the freedom to allow female altar servers. So long as the bishops and priests remain within the permitted limits, they have the freedom to make decisions according to individual preference.