A pilot-free integrated sensing and communication (ISAC) system is investigated, in which phase-modulated continuous wave (PMCW) and non-orthogonal multiple access (NOMA) waveforms are co-designed to achieve simultaneous target sensing and data transmission. To enhance effective data throughput (i.e., Goodput) in PMCW-NOMA ISAC systems, we propose a deep learning-based receiver architecture, termed two-timescale Transformer (T3former), which leverages a Transformer architecture to perform joint channel estimation and multi-user signal detection without the need for dedicated pilot signals. By treating the deterministic structure of the PMCW waveform as an implicit pilot, the proposed T3former eliminates the overhead associated with traditional pilot-based methods. The proposed T3former processes the received PMCW-NOMA signals on two distinct timescales, where a fine-grained attention mechanism captures local features across the fast-time dimension, while a coarse-grained mechanism aggregates global spatio-temporal dependencies of the slow-time dimension. Numerical results demonstrate that the proposed T3former significantly outperforms traditional successive interference cancellation (SIC) receivers, which avoids inherent error propagation in SIC. Specifically, the proposed T3former achieves a substantially lower bit error rate and a higher Goodput, approaching the theoretical maximum capacity of a pilot-free system.