A properly modified motor:
Lightened & modified piston and sometimes lighted crankshaft for less vibration
Modified port timing for your intended running RPM
Aftermarket insulator block
Aftermarket air filter
Add $45+ on to the cost of stock engines for an aftermarket air filter and insulator, you should consider them a necessity to prevent air leaks and provide proper air flow for the the higher RPM's of a heli engine.
If you are light sport flying (low RPM's) and you happen to get a Zenoah where the OEM tolerance are OK, then a stock engine may satisfy your needs. A stock engine was designed to run at 8000-9000 RPM's, a heli engine is typically running at 12,000-14,000 RPM's.
If you get a Zenoah where the truing/balance is not ideal and/or you desire to have performance, then a modified engine is better. The modifier must be familiar with heli engines, car and boat engines have different requirements.
CAUTION - my posts are based on my experiences, yours may be different.