Merging ssu-align alignments
I think this is more to do with tree building than alignment construction.

I believe the underlying issue is the 1) distribution of indels, this results in a blockwise deletion in the resulting phylogeny and 2) nucleotide saturation.

Indels Thus, for indels

Archaeal 
XXXX----YYYYY
bacterial
----ZZZZYYYYY


The resulting phylogeny will be based on YYYYY and XXXX is ignored. 

The alternative explanation is that the genetic distances involved have resulted in saturation of the nucleotide sequences. SSU has to be a nucleotide phylogeny and the level of reversion mutations over a vast amount of evolutionary time can become indistinguishable from random. 

With regards the first point, you can replace the indels "-" with "N". This is a cheat to trick a tree building program into not discarding the indel. Model based tree building programs have no ability to create a genetic distance between a base pair and an indel, so this data is essentially discarded from the tree. Worse it will remove the site from phylogenetic inference - which can be a massive loss of data. Two notes one this,


Some max. likelihood, Bayesian tree programs can avoid blockwise deletion, I don't know programmatically how they do this; 
In PAML the distribution of indels was modelled, it doesn't appear to have been widely adopted however, but might be of value.


Alternative The alternative method is really for protein genes and called "RY" coding, it might work on SSU because of the compensatory mutations involved in maintaining a secondary structure of the SSU.

Word of warning, the saturation may be so great, very little nucleotide point mutation is preserved. Essentially we are talking about preservation of phylogenetic signal across the origins of life ... and that is a very, very long time ago.