My issue is only when using the magnetic charging cable. The time it takes to charge with that cable decreases as long as I supply a higher 2.5A than when I charge it with the 1A on my external battery. But when charging using the USB 3.0 ports on a desktop from the front, it seems to take longer.

The USB ports on a desktop computer aren't dedicated charging ports, they are data ports, so while they can supply power they wont supply as much as you need.

https://en.wikipedia.org/wiki/USB_3.0#Power_and_charging

That aside if the magnetic cable you're using can't charge as fast as the standard bundled cable from a 2A or greater power supply, then your magnetic cable either isn't rated for high current, or something else is wrong with it.

There are some cool and inexpensive little gadgets that can shed some light on what's going on with your own USB equipment so far as power delivery is concerned. For example: https://www.amazon.com/Voltage-Precision-Monitors-Current-Chargers/dp/B01K4EQEZG/

They can add some resistance themselves but in my experience it's pretty negligible and doesn't obfuscate the overall picture. And they're fun of course :)