Question: How can I modify the STAR alignment parameters in Cell Ranger?
Answer: You can find the default STAR parameters here: What parameters are used for STAR alignment?
Unfortunately, there is no way to modify these parameters without editing the source code directly. The source code is included in the Cell Ranger software download and is also at https://github.com/10XGenomics/cellranger.
Source code for 10x pipelines is available on github.com for interested customers. However, we are not staffed to answer questions about it or provide support for modifications.