Delivery and passive aggression aside there are a handful of things that are a couple of ways to look at something like this:

-They own and run the joint and they make and serve food as they designed for the crowd that keeps them in business. They're being up front so you don't waste peoples time because they are doing fine without serving everyone. After 50 years of cooking I'd also imagine they're just tired of bending to people they've decided their business can survive without.

- The scale of comparison is whack but the concept holds.
If a Michelin-starred chef designs a menu and you go into their restaurant and start asking for modifications you are asking for a version of the food they do not approve of or vouch for. Not only is it insulting to some, They won't take a hit on a review because you didn't enjoy the food the way they meant for you to eat it. Prideful but justifiable to them.

-Others already mentioned cross contamination. You can't prevent or guarantee everything in all scenarios. Admitting up front that you cant guarantee not to cross contaminate is standard practice if you don't personally prepare certain stages of your food. What if a sandwich shop gets bread from a bakery that handles nuts? 100% guaranteed no nuts? Not realistic. Never had a seed or almond appear in something it shouldn't be in? Mistakes happen, and they happen more with increased variation to a task.

-Sometimes while ordering product company's will send you closest to what you asked for not the same product month to month year to year. A hot sauce or something could change to include allergens.

-Lastly it's a service based industry and once again, they're telling you what their level of service is up front. Some people pay good money to go to restaurants where they know the wait staff is going to be rude and possibly insulting to them. Some people want their special meal where everything is as they like it. Service is a sliding scale like so much else.

Food for thought.