I don't think there is anyway to configure bean-query to display things like you suggest. I think in practice people use something like the holdings listing in Fava which AFAIK just uses a query like this:
SELECT account,
units(sum(position)) as units,
cost_number as cost,
first(getprice(currency, cost_currency)) as price,
cost(sum(position)) as book_value,
value(sum(position)) as market_value,
cost_date as acquisition_date
WHERE account_sortkey(account) ~ "^[01]"
GROUP BY account, cost_date, currency, cost_currency, cost_number, account_sortkey(account)
ORDER BY account_sortkey(account), currency, cost_date
You are right that debugging inventory issues is more painful than it feels like it should be in beancount. I haven't used it in a while but occasionally bean-doctor (on the offending line) helps. In practice, I usually just visually/manually look at the holdings list and try to figure out what the problem is. I guess I put up with it because, at least for me, I'm not selling inventories very often so the problem only comes up once a year or so.
I'm not sure what people with tons of transactions (crypto, daytraders) do to manage it. Perhaps they are downloading everything automatically from brokers and, in practice, for them, they never run into inventory issues to debug?