Hi,
I've just had chance to look at your projects and their settings.
You have PLL selected as system clock, but PLL source is set to OFF
Please change PLL source to HSI
With these settings your system clock and timer clocks will be 48MHz
You have correctly set the Flowcode project clock speed to ...

Could it be the e-blocks2 port remapping that is causing confusion?

This sounds like wrong project or component settings. Clock speeds for example. Because delays and PWM definitely do work.
I'm not in a position to check your settings at the moment.
It looks like you have posted your HAL code version?
Perhaps if you post your Flowcode native version someone may be ...

Interesting about the Orange Pi, I've been using these for some time, although they are not as dirt cheap as they used to be.
I have one running my NAS, running on Armbian Linux, which I would recommend, as I've found it to be the most stable and supported ARM distro,
apart from Raspberry PI OS of ...

Could you try adding a property
file = "ATTINY4313_dev_board"
after the name =
(I can't remember if we need the .fcdx suffix)
And delete everything above <root>
Such that it's the first line.

I can't be sure on the details without checking on my installation and I'm not at all familiar with AVR.

Quick look on my mobile, re the first issue, I think you need to change device name="ATTINY4313' to something like ATTINY4313_dev_board to make the fcd unique. As I recall, as an alternative, there's also a 'file' option property for the device section.
Hope that helps.

You could use the output of the Flowcode "Compile to Hex" and use the GUI version of STM32CubeProgrammer.

Your hardware would need to have USB and Boot0 switch implemented.

Looks like RPI_CAL_String.c is missing the FCLsz_TEMPSTR fix and other updates - one for Ben

I've not had chance to check your zip yet.
But have you tried a full database update?
The CAL string files have had some changes recently.