Pattern division multiple access (PDMA) and irregular repetition slotted aloha (IRSA) are non-orthogonal multiple access (NOMA) protocols wherein packets are repeated across different resource elements. In this paper, first, the throughput of PDMA/IRSA is analyzed when common pilots are employed across users to facilitate channel estimation at the base station (BS). It is shown that the resulting pilot contamination greatly reduces the throughput compared to that obtained under the assumption of perfect channel state information (CSI). On the other hand, the use of orthogonal pilots can recover the performance loss due to pilot contamination. The analysis considers multiple antennas at the BS, and, hence, it also captures the performance of joint power-and-spatial domain random access based NOMA under estimated CSI. Thus, it is shown that it is crucial to account for practical channel estimation in the throughput analysis of PDMA/IRSA based systems.