Siliciclastic environment stromatolites are not as common in the rock record as carbonate environment stromatolites.
A study done on stromatolites during the Late Ordovician indicates a few reasons for the lack of preservation of stromatolites (and maybe other microbialites) in siliciclastic environments.
Early cementation and lithification are processes necessary for the preservation and growth of stromatolites. Siliciclastic environments may require carbonate alkalinity that is much more than in a carbonate environment to produce this early lithification & cementation as the carbonate cements may get replaced by silica during diagenesis.
Successful colonization in siliciclastic environments also require that the sandy substrate is not mobile (which is generally high in these environments) as stabilization of the sediment is required for the bacteria to produce these microbial layers. This is true in carbonate environments too.
The presence of translucent quartz grains present in these environments will also help these colonies as they allow the necessary amount of sunlight required for photosynthesis.
These and other reasons can be found in the article by Druschke, Jiang, Anderson, and Hanson called Stromatolites in the Late Ordovician Eureka Quartzite: implications for microbial growth and preservation in siliciclastic settings in Sedimentology (2009).
Thus, here is a case which is a reminder that microbialites are not just present in carbonate environments and the presence of burrows found along with the stromatolites in this study also indicates that burrowing organisms are not a limitation for the growth of these microbialites which initially I thought may be restricting the microbialites to more saline waters.
Burrowed stromatolites (adapted from Druschke et. al, 2009)