That has left Verstappen trailing Hamilton by a point going into the upcoming Iberian double-header in Portugal and Spain after the seven-time F1 champion secured the fastest lap in the Emilia Romagna Grand Prix.
Asked by GPFans Global to outline the deciding factors in this year's fight between Verstappen and Red Bull versus Mercedes and Hamilton, Horner replied: "It's all going to be about marginal gains.
"It's about who can develop the car effectively within the budget cap obviously, about reliability, operational incremental gains, about human performance, and about the drivers.
"That's what it should be about fundamentally, the two best drivers in the sport going head to head. I certainly hope we can sustain this level of performance.
"Mercedes, you can see the progress they've made since the difficult start in the Bahrain test. They're in good shape and they're not standing still so we need to keep pushing, trying to find performance and make sure that we have perfect weekends."
Mercedes stunned even themselves in Imola when Hamilton secured the 99th pole position of his F1 career.
For the first time, though, in the current turbo-hybrid era, Mercedes does not have the dominant car, while Red Bull can finally lay claim to starting a season on the front foot instead of playing catch up, as they have had to do in the past.
In drawing a comparison to Mercedes, Horner added: "The pace is obviously very close to Mercedes, and there are strengths and weaknesses of the cars in different areas.
"If you look at the performance on the inter tyre [at Imola], we were quicker at the beginning of the stint, they were quicker at the end.
"The wear pattern across the front looks different between the two cars, and I would say, Lewis's pace, he rode his luck, but once they were on the same spec of tyre, in clean air, they looked very, very competitive.
"Indeed, he got the fastest lap. I think he had the benefit of a DRS at the beginning of that lap, which is three or four-tenths.
"But it's very, very tight. It's about getting the most out of the car on a case-by-case basis"
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