Jehovah allowed the taking of slaves because it was an ancient custom of men. Seriously? Who is GOD here?
It was the custom of many cultures, yet the word of God was, "He who kidnaps a man, whether he sells him or he is found in his possession, shall surely be put to death." (Exodus 21:16)
The Lord set the bounds of servitude, and slavery, to ancient Israel, was far different than slavery as it existed in surrounding cultures. As one Christian apologist put it:
...slavery during Old Testament times was not what we commonly recognize as slavery, such as that practiced in the 17th century Americas, when Africans were captured and forcibly brought to work on plantations. Unlike our modern government welfare programs, there was no safety-net for ancient Middle Easterners who could not provide a living for themselves. In ancient Israel, people who could not provide for themselves or their families sold them into slavery so they would not die of starvation or exposure. In this way, a person would receive food and housing in exchange for labor.
So, although there are rules about slavery in the Bible, those rules exist to protect the slave. Injuring or killing slaves was punishable -- up to death of the offending party. Hebrews were commanded not to make their slave work on the Sabbath, slander a slave, have sex with another man's slave or return an escaped slave. A Hebrew was not to enslave his fellow countryman, even if he owed him money, but was to have him work as a hired worker, and he was to be released in 7 years or in the year of jubilee (which occurred every 50 years), whichever came first.
The law of the Lord also stipulated: "If a countryman of yours becomes so poor with regard to you that he sells himself to you, you shall not subject him to a slave's service. He shall be with you as a hired man, as if he were a sojourner; he shall serve with you until the year of jubilee. He shall then go out from you, he and his sons with him, and shall go back to his family, that he may return to the property of his forefathers. For they are My servants whom I brought out from the land of Egypt; they are not to be sold in a slave sale. You shall not rule over him with severity, but are to revere your God." (Leviticus 25:39-43)
It's also true that God watched over the animals and the sojourner. If a man planted fig trees, he could only put nets over some of them. He had to leave some unnetted and reserved to the birds of the air. And farmers could not wall off their crops from the traveler, but left them open for those who hungered. Travelers, of course, were forbidden to abuse the law and gather from these crops, so a balance was developed that worked. But all of these laws were a balance between justice and compassion.
If God exists, it is the gravest folly for us to presume to judge Him, for it is He who framed the values of both good and evil. If He does not exist, good and evil are mere concepts that are as meaningless as the shapes of cosmic dust in the heavens. They may be completely different on other worlds where evolution spawns completely different forms of intelligent life.
...does the Old Testament (Hebrew Scriptures) ever make an explicit distinction between God's commanding His people to do/practice something and His "allowing" them to do/practice something because it is an already-existing custom (to use your word)?
Yes, in the days of Samuel, the people wanted a king like the nations thereabout, so the Lord, after recommending against it, chose the best man for the job. It turned out to be a disaster. In our day, the Lord permits divorce, even though He detests it. There are also things that if we do it on our own volition are sins, but if commanded are not. Killing a people and taking their land is gross wickedness, but if the Lord commands it, it's not wickedness. The Lord, knowing all things, considers all things and knows the intent of our hearts. He knew the Canaanites were a wicked and adulterous people who passed their children through the fire, burning them alive. But when the Lord ordered their destruction at the hands of Israel, people who know nothing of their acts, or what was in their hearts, accuse Him of murder.
When the Lord ordered the destruction of a people, the anointed King, Saul, refused to kill the enemy king. The prophet Samuel then had the king brought before him. And there, even as the king pled for his life, Samuel slew him with a sword.
This debate is really about whether there is a God or not, not whether His actions are just. Again, if God exists, then He knows all things past, present and future; He knows the hearts and thoughts of all men. He is perfect. He is just. It's pointless to try to judge Him by atheistic standards, ethics or morals as those are not even binding on themselves, much less God.