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You could download the raw sequence reads (FASTQ files) and map them to the new T2T-Y. Probably it makes more sense to wait for a new release of the T2T human genome reference, as mapping to a subset of the genome increases false positives. It helps to have some genome bioinformatics knowledge to correctly handle those T2T references.

Can someone explain how "I have my whole genome sequenced by Nebula" relates to the news just now that "The human Y chromosome has been completely sequenced"?

How can someone have their whole (!) genome sequenced already when so far we weren't able to fully sequence the Y chromosome. And this person seems to have a Y chromosome.

because commercial "whole" genome sequences aren't really whole. But, they normally deliver the raw reads to you in a 50+GB file so I suppose you could take the reads in that file that don't map to the previous reference and try to map them to the new one. Unless you are an expert it's unlikely you would get any actionable results.

BWA-MEM is a good alignment tool. Then you can view the .bam file in IGV.