I did not find the full schematic and it appears they have provided only a partial schematic.
Briefly looking at the PI Zero, it appears the board takes 5VDC (either via the connector or USB) and has an on-board regulator that generates 3V3 and 1V8.
The 3V3 and the 1V8 power the processor.
If the processor GPIO rails are 3V3 (likely) having a 5V (minus the diode drops) appearing at the GPIO would be "danger" territory. I can't really tell the intent without studying the OPs diagram or the PI documentation.
Here is a note from the other PI variants:
The internal diodes shown in the figure are not really substrate diodes, but they are actually parasitic FETs. Electrically, their I-V characteristic looks like a diode's, but with a greater forward drop and a more gradual knee. They may protect against low current transient events caused by transient out-of-range voltages applied to the pins, but they are not intended to protect against the application of voltages greater than the supply voltage or less than ground, even with an external series resistor. In brief, you should never deliberately forward bias those "diodes". Consequently, you can not safely place an external pull-up resistor to 5V on the I/O pin. That would forward bias a parasitic FET and owing to its poor internal impedance to the chip's internal power rail it may overheat, or worse, it may bias up parts of the chip to voltages greater than they can handle. So, don't do it!
On the relay board, I can not tell what optoisolator part number is and would not be able to determine if any drop is sufficient to bring the IO voltage under the rail voltage. Typically protection diodes on the processor are designed to start conducting at some 3V3 + drop. Maybe 1V over the rail for instance. Might be in the documentation. They will also state things like 5V tolerant IO if it safe otherwise they will not. The other question would be if the optoisolator would be able to operate from a 3V3 supply.
Look around to see if the IO are open-drain. I kind-of doubt. The OP may be doing this purposefully and he may have some further insight.
Besides that, there are certainly relay boards specifically for the PI as well. This one, I think, was targeted towards the Arduino.