system bit rate vs channel coding
Both indicators are used. It depends what you mean in speaking of your indicators.
One of common usages is to compare systems where we use indicators of the same type. For example,

to compare 5G NR and LTE RANs, we usually use max throughput which is defined as the multiplication of number of antennas, number of subcarriers and QAM order per subframe. There is no error probability here.
To compare channel decoders e.g. iterative belief propagation LDPC decoder and Ordered Statistic decoder, it does not make sense anymore if error probability is ignored and, therefore, the code dimension (number of bits before encoding) must be used.