Any reason I cannot just switch a transformer from a 555 to generate high voltages?
Both boost converters and transformers can give higher voltage from lower one. Here are some specifications:

Boost converters:


Require less space than transformers
Require more components to work
Light


Transformers:


Require more space
Require less components to work
Heavy


According to this, if you want to use less space, use boost converter. 
If you can afford more space, then use transformer.