How semi-synthetic cell with artificial DNA works
The altered E Coli still only made use of the regular 20 amino acids (presumably).

Looking at the original citation, Malyshev et al didn't characterize the RNA in their altered E Coli at all. All they did was add free X and Y to the E Coli's growth medium and add a gene to the E Coli that expressed an algal nucleotide triphosphate transporter. Malyshev et al then demonstrated that replication (copying of the DNA) proceeds normally and in such a way as to preserve the X and Y content.

So no information as to whether any of the products downstream from the DNA (ie mRNA, proteins, etc) were affected by their modifications.