You can simply use the QuickTime Animation codec (bit depth 32) that you already have in Media Encoder, but if you do install the Matrox codecs, do so with Premiere closed, then next time you go to Media Encoder, choose "AVI" as the format and then under the VIDEO tab, look for CODEC and from the drop down there you can choose the needed type of Matrox codec, such as "MPEG-2 I-Frame HD + Alpha". Note that you may need to manually configure the settings, such as "1920x1080, 1.0 square pixels, upper field first" or whatever suits your project needs. You can also drop the data rate down to the minimum for the time counter export, as there is not much data to compress.
Thanks
Jeff