How to correlate two zero inflated bedgraph-like signals?
Honestly I'd just use multiBigwigSummary and then plotCorrelation from deepTools for this, but I'm a bit biased. There, the idea would be to consider each gene as a unit (you could instead use bins, but I don't think that would as nicely do what you want), namely by giving the tools a BED or GTF file input. It would then calculate the average signal in each gene/transcript and you could do your spearman's correlation. Features with 0 in all samples could optionally be removed (plotCorrelation --skipZeros).

While you certainly could go the whole 9 yards and use per-base comparisons, that seems a bit overkill and I suspect that it won't really yield appreciably more information (especially when one considers the additional time overhead).