Sounds odd, no doubt, but you talked to two different Pros at the club, and the Pro in the shop is not the Pro asking for the upfront money. That man probably has the title of Director of Golf.
There could have been a lack of understanding between these two. Some friends of mine ran into a situation where the Pro at a club they were thinking of joining told them the initiation fees would be waved if they were members at another club. They didn't ask, and he didn't tell them, that their 'membership' at a public course, really a 'season pass', did not qualify. They eventually joined, but were a bit upset at first.
The club in your example may have been offering a deal, like no initiation fees for joining in mid-summer, where they were deferring those membership fees to the next season in the hopes of picking up some dues payers for the present season. It's not unusual to see an offer like that, i.e, giving a player access-for-dues mid-season and with no other fees due until the next season. There are also clubs who are stretching out the time required to make an initiation payment. The Pro in the shop is reciting the present circumstances, i.e., no initiation fee mid-summer, but relying on anyone at a club other than the membership director to give you precise information can cause confusion and lead to upsetting outcomes.
The request for a down payment just seems to be badly handled, as I don't think I'd be willing to hand over 1k to a club so it could "pay some bills".