Should we take into account of GPU while Coding ? No way, The OpenGL API is a layer between your application and the hardware.
This is largely correct for desktop graphics as all GPUs are immediate renderers, however, this is NOT the case in mobile graphics.
The Mali GPUs use tile-based immediate-mode rendering.
For this type of rendering, the framebuffer is divided into tiles of size 16 by 16 pixels. The Polygon List Builder (PLB) organizes input data from the application into polygon lists. There is a polygon list for each tile. When a primitive covers part of a tile, an entry, called a polygon list command, is added to the polygon list for the tile.
The pixel processor takes the polygon list for one tile and computes values for all pixels in that tile before starting work on the next tile. Because this tile-based approach uses a fast, on-chip tile buffer, the GPU only writes the tile buffer contents to the framebuffer in main memory at the end of each tile. Non-tiled-based, immediate-mode renderers generally require many more framebuffer accesses. The tile-based method therefore consumes less memory bandwidth, and supports operations such as depth testing, blending and anti-aliasing efficiently.
Another difference is the treatment of rendered buffers. Immediate renderers will "save" the content of your buffer, effectively allowing you to only draw differences in the rendered scene on top of what previously existed. This IS available in Mali, however, is not enabled by default as it can cause undesired effects if used incorrectly.
There is a Mali GLES2 SDK example on how to use "EGL Preserve" Correctly available in the GLES2 SDK here
The reason the Geforce ULP based nexus 7 works as intended is that, as an immediate based renderer, it defaults to preserving the buffers, whereas Mali does not.
From the Khronos EGL specification:
EGL_SWAP_BEHAVIOR
Specifies the effect on the color buffer of posting a surface with eglSwapBuffers. A value of EGL_BUFFER_PRESERVED indicates that color buffer contents are unaffected, while EGL_BUFFER_DESTROYED indicates that color buffer contents may be destroyed or changed by the operation.
*The initial value of EGL_SWAP_BEHAVIOR is chosen by the implementation.*
The default value for EGL_SWAP_BEHAVIOUR on the Mali platform is EGL_BUFFER_DESTROYED. This is due to the performance hit associated with having to fetch the previous buffer from memory before rendering the new frame, and storing it at the end as well as the consumption of bandwidth (which is also incredibly bad for battery life on mobile devices). I am unable to comment with certainty as to the default behavior of the Tegra SoCs however, it is apparent to me that their default is EGL_BUFFER_PRESERVED.
To clarify Mali's position with regards to the Khronos GLES specifications - Mali is fully compliant.