Sure , depending on the size of the bacterial genome in question and the depth of coverage you are aiming for (especially for the RNASeq).

Just remember to use different adapter indices/barcodes for each library (and check the "colorspace" of the selected indices to verify that they are different enough), and adjust the relative amount of each library in the pool to reflect the relative seqeuncing depth you want for each (we often sequenced 10 bacterial genomes or more on a single MiSeq run).

To further reduce the danger of cross-talk you could even use dual-indices for your libraries.

I would use the lowest sequencing depth for the 16S Amplicons (probably only 0,5-1% of the pool) and divide the rest among the genome and transcriptome.

I think Illumina's protocols suggest not mix RNA and DNA at the same run...

You should talk the Illumina representative. Typically, it might not work due to low complexity of 16S sequence that would.impairs the detection of genomic sequence fragments.