Coverage calculation: long reads (RNA-seq)
The read length is irrelevant when calculating the mean coverage statistic. It's simply the total number of bases sequenced divided by the target Xome length.

In the example provided in the question, $L*N$ is equivalently expressed as $\sum^{N} l_x$, or the total length of sequenced reads. For equal-length reads, this is easier to calculate as number of reads $*$ length of reads, but the full sum is necessary if read lengths are not equal.

For what it's worth, this value, $L*N$, is also equivalent to the average read length multiplied by the number of reads, i.e.

$$\frac{\sum^{N} l_x}{N} * N$$

... which makes it a bit more obvious why the total length of sequenced bases is very slightly easier to calculate.

In answer to the second part of the question, $N$ should ideally correspond to only the sequences that are from the reference. For an assembly, only the reads that were used to create the assembly should count when considering coverage. When there's no likelihood of contamination (and especially for RNASeq with variable coverage per transcript), a statistic using the total number of reads should be good enough for most purposes that I can think of. High-throughput sequencing is such a fuzzy process that a few tens of millions of bases here or there shouldn't make a difference.