Most people wouldn't see much or any difference between standard Republicans and the alt-right (for better or worse). They'd see someone with an R next to their name and come out to vote against them, because they threw their lot in with a shitty president and party.
Every time there's a big wave (like what we could see in 2018), incumbent Congresspeople everywhere try running away from the president as if it will do anything for their chances, and it almost never does. All the conservative Southern Democratic congressmen who got blown out in 2010 are equivalent to today's suburban Republicans, who thrive on appearing bipartisan and appealing to voters' desire for "checks and balances" (ie I want a Congress who prevents the president from doing everything he wants to do... which over the last years meant preventing him from doing ANYTHING). Now Trump is president and they have to answer for it.
Put it like this: in Minnesota's 3rd Congressional District, Clinton won by 9 points while the GOP Congressman, Erik Paulsen won by 13 points. All those split-ticketers thought Clinton would win easily and wanted to send their Republican Congressman back to fight her when she pushed policies that were too extreme. He could still very well win, but now that dynamic is going to be reversed, and the usual base of voters will likely not turn out as highly as usual.
