"Missing Shipment" was renamed "The Peddler's Fate" a while back, you're playing an older version. The current one is v3.12, with another update due in the next 2-3 weeks or so.Good game overall but there are some things I dislike about it.
There are these things called "side quests" and they give the impression that "they are not related to main quests/storyline so it's optional to do them" but they are not. There is this quest called "missing shipment". It's one of the first quests and requires to you have sex with an (ugly) ogre to complete the quest. Preferably there should be an option to complete the quest without having sex with her, but even if there isn't such an option I wouldn't make a huge deal out of it and simply leave the quest unfinished. But later in the game, you get a main quest that requires getting a dress for Erevi but you can't because you didn't finish totally unrelated side quest. This is only one of the examples.
I mean, preferably I don't want to trigger any bestiality scenes and would want to have an option for that. But even if Beth's entire existence revolves around doing it with a horse thus adding such an option defeats the purpose then that should only prevent you from seeing Beth-related events/scenes/quests. It shouldn't affect completely unrelated quests that you are unable to take (and progress further in the game) unless you see some horse action.
I only didn't complete 3 side quests (missing shipment, spyglass and female goblin quests) and became unable to progress further (I can't get "restoring the temple" quest). That female goblin returns like nothing happened even if I take her ears and kill her. That's some side quest ya.
Regarding your specific comments:
1) The game explores a lot of kinks & fetishes. A LOT. No one expects any particular player to find all of that content appealing.
2) Some Side quests have to be completed before certain Main quests are available, but any additional quests in that storyline don't have to be done. For example you need to get Rosy's bakery up and running but don't have to pursue her storyline past that.
3) You don't have to peep on Beth at all, let alone get the spyglass. I made that mistake myself. Just get her Affection high enough (though she only agrees to a date with you after Restore The Temple is done). It's a lot of shoveling, but it works.
4) You do not have to return to Maghda (the ogress) after that first time, but you need to get Edgar's stuff back so he can open his shop. You'll be buying outfits from him even if you avoid as many side quests as you can. That includes Main quests...you have to complete Shopping (for Erevi in the Tower) before Restore The Temple is available.
5) Goblins are a recurring threat. They were nearly wiped out 20 years ago and now they're back. You can't reduce their threat without following their quests. If you don't, you accept they will continue to be an issue in the game. (The goblins questline is extremely popular, thouh.)
Other Side questlines don't have to be done at all. For example you can complete the game having done zero content for Mia, Victoria, Alice, the giants, or the goblins (and this list is incomplete...). However, nearly all the Side girls' questlines provide some kind of in-game benefit if you follow them. Passive income, access to more ingredients, the ability to buy things you normally can't buy, etc.