I can reproduce on an iPad Air 2 running iOS 9.3, but I think the signs are pointing to a mobile Safari or graphics driver bug. I also cannot reproduce on Chrome, Firefox, Edge (on Windows 10) or Chrome for Android, or Safari 9 on a Macbook. This suggests the Construct 2 code is correct (since it works across a broad array of browser engines, OSs and graphics hardware) and that it's possibly not a Safari bug (since it works on OS X). It could possibly be a Safari bug that manifests in the mobile variant only, or a graphics driver bug (I think iOS devices same the share similar graphics hardware/drivers, and while iOS is generally good on driver quality, our past experience is all drivers have buggy behavior at some point).
Your simpler example uses a third-party effect, which we cannot accept in bug reports. (There's a built-in replace color effect anyway?) I think your theory about transparency turning black is probably correct, but to investigate further can you provide the simpler demo with no third-party addons?