Real-world time series data are inherently multivariate, often exhibiting complex inter-channel dependencies. Each channel is typically sampled at its own period and is prone to missing values due to various practical and operational constraints. These characteristics pose fundamental challenges related to channel dependency, sampling asynchrony, and missingness, all of which must be addressed to enable robust and reliable forecasting in practical settings. However, most existing architectures are built on oversimplified assumptions, such as identical sampling periods across channels and fully observed inputs at test time, which often do not hold in real-world scenarios. To bridge this gap, we propose ChannelTokenFormer, a Transformer-based forecasting model with a flexible architecture designed to explicitly capture cross-channel interactions, accommodate channel-wise asynchronous sampling, and effectively handle missing values. Extensive experiments on three benchmark datasets modified to reflect practical settings, along with one real-world industrial dataset, demonstrate the superior robustness and accuracy of ChannelTokenFormer under challenging real-world conditions.