I'm not a Japan specialist but I am somewhat familiar with this period. While you're right that there were retainers who were more senior or had larger domains, you gloss over the important distinction between daimyos who had more land and troops and prestige (Mori clan for example) and retainers who had more influence.

Ishida was one of the Five Commissioners who were basically chief administrators for Toyotomi. These were men who were loyal retainers of Toyotomi since early days, sometimes dating back to when Hideyoshi first became daimyo himself in the 1570s. These were men whose job was to carry out Hideyoshi's orders and also gave him advice. In effect they were his cabinet of sorts, with Ishida being largely responsible for administrative matters. The commissioners worked with Hideyoshi intimately. Their influence and power were largely derivative of Hideyoshi. While Ishida only had a smallish domain of 190k koku, his influence at the Toyotomi court was far more significant.

In contrast, a lot of the daimyo who had large domains were only nominally operating under Hideyoshi while enjoying a lot of independence. They didn't spend all that much time in Osaka and were not usually involved in Toyotomi affairs. Some, like Tokugawa, was always seen as a bit of a threat or enemy by Toyotomi insiders like Ishida. When Tokugawa became regent there was a lot of tension and mistrust there, not all of which was misplaced.

So to answer your question, it basically came down to a significant difference in the type of retainers there were and the special role that some like Ishida had played in this. It wasn't just about who had more land. Although Ishida obviously knew he didn't command the respect needed, and had to involve someone like Mori to serve as figurehead leader. So Ishida didn't exactly "rise to the top" as you suggested, but he was already in the inner circle of trusted retainers long before Sekigahara in terms of closeness to the Toyotomi clan