The most important difference between the occupation and apartheid is duration. For two-state Zionists, the status quo in the West Bank is temporary, and thus cannot be truly analogized to apartheid, which was intended to be permanent. (Of course, the occupation has now lasted 49 years, beginning to approach the 66 years of apartheid.) The occupation is unjust, but it is meant to come to an end once both sides concerns about security, borders, autonomy, water, justice and so on are addressed. And of course, as to why that hasnt happened, theres blame enough to go around on all sides.
But for the 42% of Israelis who no longer believe in two states, the status quo must be regarded as the permanent status (omitting the even more shocking policy of population transfer, aka ethnic cleansing). Thus we must ask anew what, if anything, differentiates the occupation from apartheid.
Like the current system in Israel, apartheid regarded black South Africans as citizens not of South Africa proper, but of Bantustans, 10 homelands scattered across South African territory. Since blacks were citizens of these Bantustans, they didnt vote in South African elections. There were heavy restrictions on movement and land ownership. And the nominal autonomy of these Bantustans couldnt disguise the brutal disenfranchisement and segregation that they represented.
These aspects are not so different from life under permanent occupation. Nominal citizenship in another country indeed, one recognized by the United Nations but a country without some of the most basic components of statehood, like territorial integrity, self-defense and free movement. Even within nominally autonomous Palestine, ultimately the Israeli military holds sovereignty. It can go wherever it wants, regulate travel, allocate resources. While Palestine governs itself from day to day, in cases of conflict the Israeli military holds nearly all the power even in areas of supposed Palestinian autonomy let alone the vast swaths of the West Bank under full Israeli control.