I'm able to process RNA-Seq data using Rsubread to obtain feature counts after using the align function. I can also identify exon-exon junctions and fusions after aligning using the subjunc function. Is it acceptable (to save processing time) to apply featureCounts() to the subjunc BAM files? Will this produce different feature counts than I would get if I used the align function instead?
You will get slightly different counts. Subjunc is more stringent in read mapping in order to control errors in calling exon-exon junctions. If your analysis requires the identification of exon-exon junctions, then you should use Subjunc.
We typically use Subread aligner (align()) in our gene expression analysis pipeline. But there should be only minor difference in the list of differentially expressed genes identified from using the two aligners. The two aligners use the same mapping paradigm (seed and vote) to align reads.