Even if bowtie and bwa were slightly inferior to some other program, it would still likely be smarter to stick with the popular programs. That way, when you say "I aligned with bwa", people understand what was done. If you have issues you want help with, lots of people know bowtie and bwa, not so much other aligners.
Anyway, small genomes are not uniquely challenging. Your genome does not have large 100 kb repeats or near repeats. I bet it does not have regions which have extreme GC content. Your reference genome is likely very close to perfect across its whole length, and your coverage is likely pretty even, and pretty high across its whole length. You don't need boutique software to deal with data like that.
Anyway, small genomes are not uniquely challenging. Your genome does not have large 100 kb repeats or near repeats. I bet it does not have regions which have extreme GC content. Your reference genome is likely very close to perfect across its whole length, and your coverage is likely pretty even, and pretty high across its whole length. You don't need boutique software to deal with data like that.
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