The most likely reason you need to meet stricter zoning requirements when renovating your building than a store down the street is because the zoning laws have changed. At any given time, there are a variety of requirements imposed by state and local zoning regulations. However, these regulations can change and can be altered at any time by those in charge. If the regulations are changed when someone is already living in or operating in a certain location, the existing business or residence is able to operate under the old regulations and is "grandfathered in" since it would not be fair to change the zoning requirements after someone has already bought and built.
Zoning laws and building codes are designed to encourage good practice and to ensure safety during renovations. When a change is made in standard building practice, or when technology evolves, the zoning laws may change and evolve with it. Likewise, if a practice that was thought to be safe later appears to create problems, the zoning law can also change to reflect what has been learned about building.
This means that while it can seem difficult or burdensome to comply with all these zoning standards, it can often be to your benefit in the long run. By complying with all of the new building codes and requirements, you are creating a safer place for your workers to work in and for customers to come to. This can save you from potential future liability from workers comp claims or lawsuits. Further, you can rest assured that if the zoning standards change again to become even more stringent after your place is built, you too will be "grandfathered in" just as the store down the street likely was.
If you are concerned about any of the zoning requirements imposed on you or if you worry that those requirements will be too burdensome, it's in your best interest to consult with a lawyer for help and advice.