To clarify the options for solution, what you did was retain the Speeduino IdleOut circuit intact, adding a 5V pullup. The advantage to this is simplification, using the existing outputs and wiring connections of Speeduino. It results in a proper 0V-5V square-wave to the ETC as required, although it is inverted. Invert the operation in TunerStudio.
The alternative is to take the output directly from Mega D5, by disconnecting R47 from Q5 pin 2, and sending that signal from R47 to the ETC idle pin. The D5 output is already 0V-5V, and not inverted. However, to get the signal out of the Speeduino board into the wiring harness either requires removing other IdleOut components, or simply not installing them if building the Speeduino board with ETC in-mind.
I hope that makes sense, and highlights ETC is similar to any other component you use. What does the signal have to look like for the component to operate properly, and how do you configure Speeduino and its circuits to provide that? Rock on!