Mapbase actually makes some direct changes to the I/O system itself, particularly when it comes to how entities handle input parameters.
Improved Conversion
Inputs that take a specific type of parameter (e.g. SetValue on math_counter requires a number) often have to convert data to their desired "type" internally. This is mostly a programming thing and usually isn't something mappers have to worry about, but this conversion process is vital to making sure an input correctly receives and acts upon its parameter.
By default, the conversion system has a few problems that are sometimes hindering or annoying under certain circumstances. For example, if you try to pass an empty parameter to a math_counter in an attempt to clear it, it will only throw a "Bad input/output link" warning in the console. In Mapbase, however, the conversion process now better recognizes "blank" parameters, so the math_counter will properly register the empty parameter as blank and reset to 0.
There was also apparently an issue where something like a number outputted by a math_counter could not be used in an input that could take any type of text. That has been fixed as well.
Miscellaneous
This section covers a few miscellaneous changes that are a bit more niche and harder to understand if you don't know how this stuff works internally.
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FIELD_EHANDLE supports !activator, !caller, and !self
Inputs that take a specific entity handle can now use !activator, !caller, or !self.
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FIELD_EHANDLE can find entities by classname
Inputs that take a specific entity handle can now take a classname string and find an entity by its classname.