I've checked your asset. It's 256 colors, but the transparent color you want (I guess it's pink sky) is not located at palette index 0, but in the middle of the palette, that's why Tilengine doesn't show transparency. Transparency is based in palette index, not in RGB color value.
OpenTK is a C# binding for OpenGL, that is a low-level graphics API for 3D hardware. It doesn't provide the abstractions for tiled backgrounds, layers, sprites and so that Tilengine offers, so you'll have to build them yourself on top of OpenTK to get a similar functionality. But if this is easy to implement for your project, go for it!
You say you've found a bug regarding the viewport and tilesets. Would you provide sample source code and/or assets to check it? If you really have found a bug, I cannot debug and fix it without reproducing it first...
Thanks for your feedback and good luck too!