I'm afraid that I might write something silly when I write about the RC world. So far no one with RC knowledge has joined 
In the Arduino world a PWM signal is not a Servo signal. Please keep them separated.
A generic PWM signal is with analogWrite(): https://www.arduino.cc/reference/en/language/functions/analog-io/analogwrite/
The Arduino Servo library generates a servo signal. It runs in a interrupt and uses software in that interrupt to generate the servo signal on any digital pin: https://www.arduino.cc/reference/en/libraries/servo/.
Funny: 32 servos in Wokwi simulation All the signals are made in a single interrupt routine.
You need a library for PWM input. There is no official or standard library for it.
Any analog pin can be used for a potentiometer.
256k flash is a lot. You can not fill that with a sketch of a many thousands code lines.
The "MKR" series are small boards. The larger Arduino Zero has an extra usb port and a different port to upload a sketch. The Arduino M0 is between the Zero and the MKR Zero but uses its own settings. They are all very much the same.
I don't know the dimensions of the Arduino MKR Zero ! It should be somewhere 
If the PWM output needs to be 3.3V signals, then use a 3.3V board. I prefer with a SAMD21G processor, because that processor is used in my Arduino boards, such as the MKR Zero.
The Arduino Uno/Nano/Mega output 5V signals. Those signal are also very strong, up to 40mA shortcut current for a simple digital output pin. That is enough to damage 3.3V sensors or other 3.3V components.
I don't care how many amps you have. I suggest to add a fuse or polyfuse to prevent that a shortcut will cause a fire. Some Arduino boards have a 500mA polyfuse between the USB 5V power and the board. Since 100mA might be enough for the Zero board, a polyfuse of 500mA is a reasonable value.
It is possible to power a Arduino board with 5V. Some say it is not recommended, and some prefer it. The Arduino MKR Zero is something special. It only accepts 5V at the VIN pin.
The larger Arduino Zero board has a onboard DC/DC-converter to make 5V and then a voltage regulator for 3.3V. If you have 5V, then the safest way is to apply that 5V via a USB connector to the board (only one USB connector can accept power). I see other possibilities, that those might not be 100% safe.
The MPU-6050 is outdated and noisy and your MPU-6050 might be a counterfeit.
Arduino user @jremington has selected a good sensor and make a library for it: https://github.com/jremington/LSM9DS1-AHRS
I don't know where to buy RC things.
A prototype shield can be handy to connect wires to the Arduino. I solder the wires, then I attach the wires firmly to the prototype shield and then I put hotglue over it.
Some mechanical damping for the accelerometer/gyro will help a lot. They are very sensitive for vibrations and short shocks.
You can make your own format for Serial/UART communication.
Where did you read about a "digital port" ? There are "digital pins" and "digital pots" and the manufacturer sometimes refers to the internal hardware for a digital pin as "digital port function". I suggest that you ignore the term "digital port".
Arduino started with a "documentation" section and now it is very confusing. Sometimes the documentation for a board is spread over 4 or 5 page. A single page in the store with details and one more "Getting Started" page would be enough.
If you mention something, could you give a link to it ?