The custom roles in data() ignoring the column isn't necessarily a problem, but combined with the callers not knowing what is in a column it gets problematic. e.g. if you look at the Delegate's paintText, it wants to do different rendering based on the "meaning" of the column but ultimately needs to hardcode the columns because there is no way to determine it programmatically.

If you made data() fully index and role aware you could turn the Delegate from

switch (index.column()) {
case 1:
    state = index.data(PackageModel::StatusRole).toInt();

    if (state & QApt::Package::NowBroken) {
        text = MuonStrings::global()->packageStateName(QApt::Package::NowBroken);
        pen.setBrush(color.foreground(KColorScheme::NegativeText));
        break;
    }

into this, by basically moving all the switch casing into the model's data():

text = index.data(Qt::DisplayRole).toInt(); // Internally: MuonStrings::global()->packageStateName(m_package.at(i)->state());
pen.setBrush(index.data(Qt::ForegroundRole)); // Internally: switch(m_package.at(i)->state()) { ... return color.foreground(KColorScheme::NegativeText) }

BUT

this ultimately moves most of the theming decision going on into the model. All the code would still be there, just living in the Model somewhere.
The current code takes a different approach in that it makes the theming decision in the delegate (which IMO is better UI/logic separation).
Either approach is fine and basically the same amount of code (albeit in different files). The current code's main deficiency is with assigning meaning to columns though. i.e. a proper implementation of delegate-side theming would have to be something like:

NewFancyColumRoleEnum role = index.model().headerData(index.column(), Qt::Vertical, NewFancyColumRoleEnum);
switch (role) {
case StateColumnRole:
    state = index.data(PackageModel::StatusRole).toInt();

    if (state & QApt::Package::NowBroken) {
        text = MuonStrings::global()->packageStateName(QApt::Package::NowBroken);
        pen.setBrush(color.foreground(KColorScheme::NegativeText));
        break;
    }

Anyway, food for thought.