The difference for different voltage boards lies in the parts, that are soldered on it. Often microcontrollers support more than one supply voltage, but impose different performance limits on the system. Take for example the Arduino Uno: It uses the Atmega328p, which can run both on 3.3V and 5V. But on the UNO there is a 16MHz quartz, which generates the controllers clock signal. The Atmega328p cannot run 16MHz with only 3.3 volts. To run a board on a voltage, for which it wasn't directly build, mostly requires you to resolder it with the correct parts.
whenever i try to search about it i see people saying that most newer modules are running on 3.3v so they convert their 5v arduino to 3.3v
There are special chips, called voltage regulators/converters. They come with various working principles, but basically they are converting one voltage to another. The Arduino Uno has one connected to Vin, so that you can apply between 7V and 12V to Vin and the Arduino itself will only see the 5V it get's from the regulator. Some modules also have a voltage regulator, but not all. Be careful not to provide more than the specified voltage to any board or you may destroy it.
the arduino I bought looks like it has both! is that even possible?
First, as Juraj wrote, this is not an Arduino. It is an ESP8266, a totally different chip and board. But you can also program it through the Arduino IDE, without it being an Arduino. Second: When they write, that you can provide it with either 3.3V or 5V, they mean, that you can provide 5V through the USB jack and a voltage regulator will convert it to 3.3V for the ESP, which runs completely on 3.3V. You should not connect 5V to any other pin.
since this arduino says vin is 5-12v the two should connect and work properly, right?
As stated above the 12V is only, what you can at maximum provide at Vin. The ESP8266 runs on 3.3V, so you will have to provide 3.3V (or more over the Vin pin). The LED matrix runs at 5V, as you stated. So you need a 5V source and a level shifter for the 2 lines between the ESP8266 and the matrix. If you connect them directly, you would damage the ESP8266. So: No, you cannot use it directly. It is up to you, if you want to use a level shifter or buy another matrix display, which can be controlled by a 3.3V signal.