Why do you see it as conflicting?

Lucheni was a poor child that went through different foster homes throughout his childhood and rarely had a chance to even go to school properly. He joined the Italian Army mainly because it provided him with clothing and several meals a day, something he did not regularly get to experience otherwise because of his poor work ethics. He also had a lot of problems with his superiors in the army because of his constant disobedience.

I'd call him very much an anarchist. He hated the aristocracy in general and was just out to kill any one of them to become a paragon of resistance against what he perceived to be a parasitic social class, there was no specific resentment against the Habsburgs I am aware of. Unfortunately for him, he was not just a worker, he was a bad one at that and never able to stick with a job for too long so he had absolutely no funds to spare for traveling to his victim and consequently had to wait at home for them to come near him. Hell, he was so poor he couldn't even afford to purchase a gun or even knife and had to settle on sharpening a file.

He had plans to kill others before the Empress, but these plans fell through for various reasons and only when he learned that the Empress Sisi was visiting (under the guise of Duchess of Hohenembs, which didn't fool the press) did he decide on her. Possibly also because she was known to regularly refuse security escorts.

During Lucheni's trial he repeatedly asked for the death sentence for himself with the argument that "whoever doesn't work, doesn't deserve to live", obviously not just because he wanted to become a martyr for his cause but also a stab at the aristocracy. Geneva didn't have capital punishment though, and his requests to be transferred to Lucerne who still had were denied, so he just got life in prison, where he hanged himself after 12 years in 1910, much to the relief of everyone there since Lucheni had repeatedly tried to attack probably every single one of them.