Need help in codon optimization
Generally the codon optimization is the most frequent tRNA found in your species of interest. However, your codon must not result in something that disrupts standard molecular biology practices. For instance, if your codon places a restriction site in a unique cloning vector, then the algorithm will just look for the next best codon which does not cause unwanted addition or elimination of a cloning site. Places like IDT will also weigh the cost of the codon vs. the ease of manufacturing in their algorithm (see here.)

What you describe as translational pausing that is 'needed' by the organism to optimize proper gene expression is a consequence and not a necessity of infrequent codons (to my full understanding). See here. That means you don't want to add this translational pausing in optimized gene expression. It is a simply an evolutionary byproduct. 

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To answer your question more bluntly, I can tell you with some experience to trust the codon optimization algorithms from biotech companies like IDT. I find they work very well. Rice is a common enough organism :)