I didn't fully understand your question (specifically, the last part), but hopefully this gives you an answer:
The more transactions included in a block, the more likely it is to be an uncle due to propagation delays. More precisely, the more gas consumed, the more likely the block is to be uncled (resulting in a reduced reward for the miner). Therefore, it is not always in the best interests of a miner to include transactions. Certain EVM instructions may also take longer for a particular node to process (for example, maybe the computer has a particularly poor implementation of Keccak but very fast disk I/O); an algorithm could make use of that information and change the transactions to be incorporated into a block on-the-fly to minimize the time required to find and propagate a block. Mis-pricing of instructions relative to one another led to a denial of service attack on Ethereum in 2016.
Thus, it is possible that a miner's node may believe a transaction to be unfairly (or at least not advantageously) priced and thus not include it. Even though the maximum reward for mining a block with a transaction is higher than mining a block without it, the expected value might be lower. The node could also just be very conservative and avoid adding many transactions just in case they might lead to uncles.