Would two species of yeast with similar genome sizes have the same number of genes or chromosomes?
This question appears to start from the premise that different species of yeast are closely related, but they aren't. Saccharomyces cerevisae and Schizosaccharomyces pombe, both Ascomycetes, are thought to have diverged at least 300 million years ago (c.f. the mammalian divergence from other vertebrates was about 200 million years ago).

S. cerevisiae has a genome size of 12.1 Mb, with 5821 protein coding genes (plus another 786 dubious ORFs) spread over 16 chromosomes.

S. pombe has a genome size of 12.6 Mb with 5124 protein coding genes on just 3 chromosomes.

Filamentous fungi have larger genomes and gene numbers. From memory, Aspergillus nidulans has 8 chromosomes and over 9,000 protein coding genes. So, the similarity in gene numbers in the two yeasts probably reflects their broadly similar lifestyles.