In my view, a work provided cell phone with a personal plan is not a perk - it's a burden. If your work and home numbers are the same, your employer has the power to contact you anytime they want, day or night, vacation, unless you turn off your ability to get personal calls.
To me, that's not worth the amount I'd save on my cell plan (mind you, I spend about $5 a month at most on my cell phone - but I think even $100 a month wouldn't be worth the aggravation).
A 5-10 minute window for showing up late in bad weather or other unforeseen circumstances? That's basically a standard consideration for any salaried job I know that doesn't involve strict starting responsibilities or someone needing to cover you. Of course, the reverse in a salaried job is that often you need to show up a bit early, stay a bit late, go to a lunch time meeting, answer an email on the weekend and so on.
Being allowed to take the occasional unofficial comp day when you've been working hard? That's a perk (it's one my job has - if you've been working 80 hour weeks for a deadline, and want to take a break for a day when it's done, no-body minds).
Being forced to take a random day off when you don't actually want to, and it's just means you'll have to work double speed for the next couple of days? That's not a perk, it's actually a burden. And in a two person office, I'd wonder if this wasn't my boss's way of sneaking a day off themselves.
Being able to take flexible hours for doctor's appointments? That is a perk, and not a universal one. But again, it's the kind of thing that is balanced by the days you come early, stay late, work through lunch, finish something after going home.
As an aside, the Boss's behaviour here put a social version of it in my mind. It's like your grandmother offers you her good set of dishes - the non microwave/dishwasher safe delicate 12 piece setting of china. You say thanks but you don't really have room for it in your one bedroom apartment, and you don't even have a dining room table. But she pushes and pushes, and finally, you take it to make her happy and manage to wedge it in somewhere. Then, a couple of months later she asks you to drive three hours to pick her up for a family function, and you can't do it. So she lambasts you for being so ungrateful and selfish after she gave you such a valuable set of dishes - you owe her for that - and starts complaining about what an ungrateful witch you are to other family members.